Earlier this year, after many years of anticipation, I, too, reached Kisangani. Conrad recounted how, as a nine-year-old, he had been fascinated by the empty map of Africa and had longed to go to this country. I, too, had imagined the great walls of trees, the river sweeping 1,000 miles up from the south and then bending west towards the Atlantic, the Pygmies, the diamonds and what many writers have referred to as the "green heart of the world".

Unlike Conrad, I had to make the journey by plane. A decade of civil war that began in the 1990s has cost a conservative two million lives and led to endless destruction and political turmoil since. Central Congo is no longer at war, but Kisangani and the upper Congo are more isolated and harder to reach than they were 100 years ago. Instead of the 10 or more river boats that every day used to ply between the capital, Kinshasa, and Kisangani, there are only a few barges now.

Kisangani is not a disappointment. There's nothing left of the trading station of the 1890s, and precious little of the once-prosperous Stanleyville built for 5,000 colonials in the 20s. The whole of the city in the jungle is now crumbling in the steaming heat and most of its buildings are pockmarked after three major battles in 10 years, fought in its streets, between Ugandan and Rwandan armies.

It is a beleaguered, impoverished, shot-up hole, a dangerous frontier town with a busted economy, but it is still one of Africa's great trading centres and the Democratic Republic of the Congo's (DRC) third largest city. There are streets of diamond dealers waiting for the many miners who slip in with their small hidden packages in hope of riches; ivory traders, fishers, coffee growers, former soldiers, nuns, cloth merchants and chancers.

Perhaps 400,000 people live here today, and while the palm oil and clothing factories have shut, activity hums around the great Catholic cathedral and the mile-wide river it overlooks. There are few cars, the parks have been dug up, and roads to the city are mostly passable only on a motorbike. But the mobile phones work even if the electricity does not and the whole place throbs with life.

Apart from Kisangani's setting, above Stanley Falls, on the great bend of the river Congo, Conrad would recognise little, mainly because the dense jungle that framed his novel and reached to the edge of Kurtz's trading post is being felled at an alarming rate.

The only way to find out what is happening in Congo's jungles today is to go by boat with locals. I hook up with René Ngongo, a young Congolese academic who runs Ocean, an ecological group based in Kinshasa. With us come Stephan Van Praet, Greenpeace International Africa forest campaign coordinator, and Jean-Faustin Lakondo and Joel Bofando, two young MPs who have just been elected to Equator province's first parliament. We hire a 30ft-long pirogue, or dugout canoe, and set off down river for the village of Isangi, their home territory, on the edge of the great forest a day away.

Isangi is spread along the banks of the Congo at its junction with the river Lomami. All seems calm when we arrive, but it is clear from a meeting held outside the school at dusk that people are greatly agitated. Four years ago, Safbois, a part-American, part Belgian-owned conglomerate, was awarded a massive logging concession of more than 100,000 square miles just to the south of the town, and it is now felling the forest for the precious afrormosia tree - African teak.

One by one in the sweaty night, members of local human rights groups, churchmen, villagers and government officers stand up to condemn the company which they say will profit from their trees while providing little or nothing for them: their hunting grounds are being destroyed, their access to wild food denied, there are no jobs.

"I see the logs going down the river, and it makes me cry," one villager says.

"Our forests are being stolen from us," says another. "It is misery for the communities. Safbois has come in and is taking our future. We do not know what to do."

"With the loss of forest we have much more death and illness," says a third.

"But it is with our complicity, if foreigners profit from our forests," says a teacher.

They accuse the government of harassment and Safbois of failing to keep its promises. When a company is granted a concession from central government to log in Congo, it must sign an agreement with the local chiefs and hereditary landowners who give permission for it to extract the trees in return for development packages. In this case, on September 15 2004, Safbois signed a contract with three villages to build three schools and hospitals, to repair roads, employ some local people, and provide four motorbikes and 160 bicycles for the village.

Many recognise echoes of the past in this arrangement. In Conrad's day, Congo was the Congo Free State, the personal property of King Leopold of Belgium - later, in 1908, the Belgian state took over and it became Belgian Congo. The king, together with the explorer and journalist Henry Morton Stanley (famed for his supposed greeting, "Dr Livingstone, I presume"), devised the concession system whereby the country was carved up into vast tranches for companies to do with what they liked, so long as they paid the king 50% of their income. Stanley himself persuaded 450 chiefs to sign treaties allowing companies access to their resources. Few had any idea what they were signing away in exchange for the cloth, trinkets, alcohol and other cheap goods they were given.

"History is repeating itself," Bofando says. "We are being forced to hand over our forests for nothing. It is leading to misery."

Yafunga, four or more hours away, is one of the villages promised a school by Safbois. We make our way to the village, but there is clearly no new school. There is a makeshift shelter made of greenwood, half-covered in the thinnest imaginable corrugated iron, but it has no sides, no floor, no windows. One big storm would bring it down.

"This is meant to be the new school for 120 students," says the headteacher, Give Juvenal Lomata. "Look at it. They promised us a school and signed a contract 30 months ago. Nothing has happened. It is an insult. It would have been better if they had given us the materials. They broke their promises to children."

The villagers convene a meeting in Yafunga church. Here, they discover for the first time how much their afrormosia wood is worth in Europe. One tree trunk, Van Praet says, can sell for $2,000 in Kinshasa and, when sawn, $10,000 or more in Europe - many times what a whole village could earn in a year. They are angry and shocked.

"Did you know the value of the trees when the contract was signed?" I ask.

"No, no, no," the crowd shout.

"Did the company tell the community the value?"

"No," they say.

"Did the chief tell you?"

"No."

They send for the chief, who is in his 50s and clearly upset. "I did not know," he says. "I had no idea of the profits that can be made from the trees. A grave injustice has been done."

Almost in tears, he tells people in the church how the contract was signed. "We were forced to sign the paper. We really had no say. The meeting with the company started at 11pm and finished at 3am. The police were there and the military and the authorities. We felt threatened. We were not allowed to ask questions. It was intimidation. The next day we were told we could say nothing. We are afraid of the authorities. We had to sign it."

So we go to see Safbois, accompanied by a crowd of villagers. The company has built a small port where once there was a graveyard and a village shop on the edge of the pristine Lomami river; there is no one around. Later we find Florimont Ugalomaswa, the company's personnel officer, at its logging camp, where hundreds of huge afrormosia logs are waiting in the yard to be shipped to Kinshasa, then exported to Europe. Ugalomaswa tries to defend the company against charges that it employs few people from the villages nearby.

"When we came here we needed people with experience. We could not find chauffeurs, drivers or chainsaw men," he says. "We employ 83 people, including 30-35 day workers from the communities."

"They are paid less than $1 a day," one man says.

"Where is the school that you promised two and a half years ago?" asks an angry woman.

"The school is there!" Ugalomaswa says. The villagers laugh. "We have said we would build a school in each community, but we have had three directors of the company here in three years. The problem has been changes in management. Things happen now. We are building the schools."

"Where are the hospitals?" another woman asks.

"It was not a hospital we promised. It was a dispensary," Ugalomaswa says.

"But it says here that you will provide hospitals, plural," one man says, brandishing a copy of the agreement. "Where is it?"

"The community hasn't told us yet where to put it."

"You are joking with us," the villager says.

It is a brave but hopeless performance.

The next day we set off by pirogue back up the Congo towards Kisangani. "The European perception of the Congo as the dark heart of Africa or the world is completely wrong," René Ngongo says. "For us, the river and the forest have always been the heart of life. We are all here thanks to the river. The forest is full of riches. We have fish weighing 100 kilograms. At night it lives. People are beginning to understand that the exploitation must benefit local people. For us the forest has always been our mother. It can be compared to your supermarkets. Everyone depends on it. What is happening is that the exploiters promise to improve living conditions by cutting down the forest. It's a paradox we do not understand."

After several hours' slow passage against the current, a speedboat comes towards us in the middle of the river. Two white men and a black woman are on board. It swerves into us and nearly swamps our fragile pirogue with its wash. One man photographs us, the other steers and gives V-signs. The boat comes back a second time. This time we almost capsize. "It's the loggers," Ngongo says. "They are warning us."

In Conrad's day, 40 companies between them shared an area larger than France as their personal fiefdoms. King Leopold took 50% of the profits of all the ivory, rubber, gold, diamonds or wood that the concessionaries traded. The companies in turn used slave labour, floggings, mutilation and even murder to extract the resources. Today, the state has effectively collapsed and the World Bank in Washington has been funding the reconstruction of the country's shattered economy. It has decided to go along with the concession system.

Today a dozen large, mostly European, companies dominate the industry and have vast concessions; Trans-M has Lebanese owners; another group, which controls around 15m acres, is owned by the Portuguese Trinidade brothers; the American Blattner family has more than 2m acres; the German Danzer Group has 5m. To make worthwhile the tricky task of exporting wood over the rapids near Kinshasa, the demand is for the highest quality wood for European kitchens, floors and furniture.

Peace has exacerbated the problem, opening up the forest to smaller companies. "Logging in Congo is out of control," Ngongo says. "There is now a rush for the trees. The war protected the forests."

Greenpeace research shows that the country has been carved up, just as in King Leopold's day, and there are now 156 concessions covering nearly 75,000 square miles of mostly intact rainforest - far bigger than England and Wales put together. Kisangani is completely surrounded by concessions, as is most of the land near the rivers. In theory, the companies must pay central government nearly £9m rent a year for these concessions, of which 40% should be returned to provincial governments for development. In practice, Van Praet says, "There is very little evidence that companies pay either on time or in full, and little or nothing goes back to the provinces."

"What is at stake is enormous," Ngongo says. "Two-thirds of the people in Congo, 40 million people, depend on this forest to provide food, medicines and building materials. It is critical for the survival of the people and animals. This is also one of the biggest stores of carbon in the world, so it is critical, too, for climate change. Yet the companies are being encouraged to take what they can."

Most of the concessions, Van Praet says, have been awarded in violation of the new forest laws and after the World Bank imposed a moratorium on new concessions in 2002, in return for $90m of development aid. The government is now reviewing their legality and will decide whether to cancel them later this year. But in reality the companies know they will be able to appeal, and log, for many years.

Greenpeace and Ocean are adamant that the industrial logging concession system in Congo will destroy the forest, impoverish the people and undermine the state. "All are in areas inhabited by people dependent on the forest, many have Pygmies living in them, and a third are in areas identified as vital for conservation," Van Praet says.

The system of concessionaries offering gifts to communities in return for permission to log is now the basis of the whole forestry operation in Congo. Research by Ngongo and Ocean shows that isolated communities, which have seldom had contact with outsiders, are being persuaded to sign away, for just a few machetes and bags of salt, the rights to the forests on which they have depended for millions of years. One company gave a community 18 bars of soap, four packets of soup, 24 bottles of beer and two bags of sugar. Another signed a deal for 20 sacks of sugar, 200 bags of salt, 200 machetes and 200 spades. In Orientale province, another company promised a school, a clinic and enough wood to provide for their coffins.

"It is happening everywhere," Ngongo says. "Concessions are being given out, and the villagers are not being told what the chiefs are signing up to. Communities are in chaos and there is more and more social conflict. It is a cruel system that continues the injustices and atrocities of the colonial system but it is even worse because it deprives communities of their resources and consigns them to perpetual poverty." The concessionary system is so far found only in Africa - in francophone Africa, in fact - but it may yet spread to the great forest areas of, say, South America.

Back in Kinshasa, we call on the World Bank and see an official who asks to speak anonymously. "Clearly the companies are the root of the problem," he says. "They are taking advantage of the chaos. They exploit the poor. It's normal. They are businessmen. It's a very small group of people who get rich and the very large group stay poor. Because the government is weak, it cannot take them on. Nothing much has changed since King Leopold's day. All this started in colonial times. The government continued the same old ways after independence. It's still a system of colonialism."

Corruption, he says, is rife at every level of government and business. "Businesses pay the government," he says. "They are corrupt. You see a minister, you see the air-conditioning is not working, you say you will fix it. Or you give a present to the minister's wife. It can be very subtle. Perhaps you arrange visas for an official's children. There are hundreds of different ways to be corrupt. We, the bank, cannot replace the government, so we try to equip and help the ministries. We buy them motorbikes, computers."

He assures me that the bank does not support the companies - but this is not strictly true. Although the bank's website says its private credit organisation, the International Finance Corp, "has no client in the field of forests in DRC", it emerged last month that the IFC had invested $15m in Olam International - a Singaporean company with an annual turnover of $1.6bn that pays small-scale artisanal loggers to cut for it in Congo and has two large concessions obtained well after the moratorium. Olam said that it was unaware of the moratorium at the time it received its allotments, but in a statement to journalists said: "We will abide by the World Bank's decision about the contracts' legality."

The bank maintains full confidence in Olam, stating on its website: "Although a small proportion of overall company revenue, Olam trades in timber but promotes sustainable forest management practices and its operations are considered fully consistent with the requirements of the November 2002 World Bank Forests Policy."

Next on our agenda: the companies. Françoise van de Ven, a Belgian woman who has lived in Congo for many years, is secretary general of the Fédération des Industriels du Bois, which represents 14 of the biggest timber companies in Congo. "Are we legal? Are we illegal?" she says. "No one knows. But what I do know is that the forest is coming down. It's terribly alarming and there is no solution. It's mainly in the east of Congo and no one sees it."

She shifts the blame to small-scale logging operations. "The situation is worse than you think. Right now there are 8,000 small-scale wood exporters, each felling 50 hectares a year, mainly in the east. That's 400,000 hectares [approaching a million acres] being clear-felled a year - or five million cubic metres of wood. There could be 500 chainsaws working in one forest like Ituri. The timber goes to Rwanda, Uganda, wherever."

She blames international companies such as Olam which pay, quite legally, for the permits of these small artisans. "They give chainsaws to people, then buy the wood from them. They are doing 10,000 cubic metres a year. They only export some. It makes my heart cry.

"I have run a company in Congo, so I know how it works. If you pay all the taxes, you would not exist. Safbois pays 164 different taxes. There are so many small, stupid taxes. Some get declared on and some don't. It's normal. Taxes drive you nuts. You hit a brick wall every two weeks."

She represented Safbois at the meeting with the villages near Isangi. "You give them [people] the chance to have good housing, you give them timber and cement. But if you don't see anything come of it, it's because they have sold it on. The chiefs get the money. They wanted rifles for hunting, sugar and salt. I said, 'But in 25 years' time, when all the logs are gone, what will you say?' I tried to make them see the future.

"Safbois invested about $10,000 in that school. We had an agreement that we would supply all the bricks. We said we will build the school but we need five people to work in week one, three in week two. Nobody came. We gave them the possibility to make the bricks, but they never made them. You get very frustrated. You pull your hair out. It goes from worse to worse. There is a solution - give them work, give them schooling, give them medicines, and all this will stop."

At last we go to Safbois' headquarters in Kinshasa. The inner sanctum of one of the most powerful companies in Africa is the office of David Blattner, its financial director. It is furnished like a hotel room, with pictures of the great Congolese forests and mountains. There is a plaque, signed by President Kabila, awarding the company the highest civilian honour, the Gold Medal of the Republic. The company cuts trees, but it also builds roads and provides most of the gas for the capital city.

"Congo can only do sustainable forestry," Blattner says. "The infrastructure is so poor, and the costs of extracting wood so great, that you cannot clear-cut. We take just a few logs per acre. After five years you can't see the difference. And the money goes to the country."

Five minutes later, his brother Daniel, who runs Safbois, comes into the room with Olivier Megare, the company's production chief. Daniel Blattner is already angry: "You went [to our camp] without warning. We were shocked. It was simple politeness to ask. We have good relations with the community. We are there for decades. We are employing people. We are developing the regions, we are building schools and roads. There is no infrastructure. It's not simple!"

Soon everyone is shouting. "This country has one renewable resource. Wood. Trees are renewable," Blattner shouts. "We are working to achieve everything we agreed. We have invested money. We have paid workers. We are not substitutes for the state. We are totally legal. We are the invited in this country. We have no interest in razing the forest, just taking a few trees from every hectare. Why is it not in our interests to have good relations with the communities? Tell me why?"

He is shouting very loudly now. "There were logistical problems ... We work legally!" he repeats.

He's right - up to a point. What he doesn't say is that to take out just one valuable tree requires roads to be built deep into the forest, which means hundreds of other trees are cut or smashed down - often the very ones that the communities use and need for medicines and foods. The companies do not replant - the trees they cut down may be 100 years old - and they leave the forest vulnerable to floods of hunters and other farmers moving in to pull down more.

"You can never replace the big trees," Ngongo says. "The forest will never recover the wildlife. In Conrad's day, traders such as Kurtz took only the ivory. Now the companies are taking everything, including the chance to develop."

The situation is far from how it was in Conrad's day. Blattner is no ranting Kurtz, nor are there atrocities being carried out. The Congolese are not doomed to labour for a colonial king or a mad trader who employs slaves. What is happening, though, is unjust and ecologically cruel. The same concessionary system that Conrad found is now accepted by the World Bank and western governments. It deprives millions of people of their resources, encourages corruption, prevents development and divides communities. The real scandal today is that, for a few square metres of flooring, or a kitchen door, or a bedpost, the second greatest forest in the world is being destroyed, probably for ever.