Deep in the eastern Congo, in the thick of a conflict that plumbs the depths of human cruelty, one doctor in a single-storey hospital is keeping hope alive. Gynaecologist Denis Mukwege draws his strength, he says, from the indomitable spirit of the most weakened of victims – women raped in a calculated act of war who arrive, "broken, waiting for death, hiding their faces", at his hospital. "Often they cannot talk, walk or eat," he says.

A 14-year war that is, in effect, a continuation of the genocide that took place in neighbouring Rwanda has become a "gynocide", in which rape is used to tear the bonds of a community apart and facilitate access to mineral wealth.

In this volatile environment, 55-year-old Mukwege and his team have surgically repaired more than 20,000 women out of the thousands who have been war-raped in the Congo's Great Lakes region. "Rape," he says, "destroys women beyond the bounds of the describable."

Yet his patients keep inspiring him to strengthen his commitment. "A few years ago, a woman came to us who had been raped and had caught HIV," he says. "She arrived with her five children, and we treated her. When she left, she was given $20 to help her on her way. The other day she invited me over. She has bought a piece of land, built a house, paid a dowry for her son's wedding and has $1,000 she wants to spend on a business trip abroad. When you see the determination that can exist within someone whom one has tried to destroy, you want to fight alongside them."

Panzi hospital sits on a tree-lined dirt road in a suburb of Bukavu, the capital of South Kivu province, built by the Belgians to resemble an Ardennes town. Simple but clean and well organised, the 400-bed hospital is a haven of sanity in a sick environment. Mukwege built it up from scratch in 1999 after his previous hospital at Lemera, 300km away, was destroyed.

Mukwege is tall, his height exaggerated by his black clogs – a reminder of time he spent in Sweden, where all medical staff wear them. He has a deep voice, a ready ear and a childlike glint in his eye whenever things get tense. Pipped to the 2009 Nobel peace prize by President Obama, he is adored here and faces a barrage of greetings on his daily rounds.

On his desk, the lamp is vintage Ikea, supplied by the Swedish army. Mukwege, a pastor's son who trained in Burundi and France, drew on his contacts in the Pentecostal church to set up Panzi. "When I was eight, I accompanied my father to see a little boy who was ill. He prayed for the boy but, to my disappointment, he did not give him medicine. He said that was the doctor's job. So I told him I would become a doctor so people he prayed for would get better more quickly."

The third of nine children, he opted for gynaecology early in his career after seeing the pain endured in childbirth – especially forced deliveries due to the lack of availability of Caesarean sections – by rural Congolese women. He says his faith in God helps him to confront the depraved notion of rape as a weapon of war in a conflict where forces on all sides often share one rifle between three soldiers. "It is the work of Satan. It is evil. In a conventional war, if someone is killed by a bullet, there can be grieving and life moves on. With rape, the effects can surface 15 years later."

He believes the war in eastern Congo – which began in reprisal against perpetrators of the 1994 Rwandan genocide and has evolved into a frenzied scramble for mineral wealth, especially for the prized colombo-tantalite (coltan), crucial for the production of microchips – has been allowed to continue because of discrimination by the international community. "The indescribable events here amount to the worst form of terrorism. In any other part of the world, the international community would have put a stop to it. International justice is not doing its work here. There are people in some parts of the world who believe that other human beings – Africans – somehow have a higher threshold of pain, that they love their children less, that savagery for them is normal, or rape culturally acceptable."

A few hundred metres from the hospital, Mukwege has set up a safe house where patients, after counselling, are taught sewing, weaving and soap-making skills. Raped women need to become self-sufficient because they are often rejected by their husbands and families.

The rape survivors that pass through Dorcas House are aged between two and 80. One 15-year-old tells her story while struggling to pacify her 18-month-old son, conceived after she was taken from her village by armed men and forced to be a "wife" for several months. "I cannot go back to my village. I am afraid they will take me again. I heard recently that they took my cousins. I also do not know whether my aunt, who is my only living relative, would take me in, or accept Baraka," says the girl, who, despite having borne a son conceived in hate, gave him a name that means "blessing".

Mukwege says sexual assault is comparable to biological warfare as an extermination tactic. He says there is a policy to make fathers and children watch the rapes. To render the woman sterile, the rapists complete the brutality by firing a bullet into the vagina or shredding its walls using a rifle butt or tree branch.

There are signs that the international community is waking up to this conflict, which may have claimed as many as four million lives – more than any other since the second world war. After a frenzied attack in July in which 300 women were raped over three days in Walikale, in northern Kivu, the United Nations last month sent a delegation to investigate. In France, Callixte Mbarushimana, the political leader of the Forces Démocratiques de Libération du Rwanda (FDLR) was arrested under an International Criminal Court warrant that cites rape among the charges. But this month, claiming a renewed need to quell chaos, Rwanda has reportedly rescinded on an agreement made in September and sent troops back across the border into Kivu's three provinces.

Like many in his country, Mukwege believes the international community would rather have a war-ravaged Congo that can be pillaged than one that, by its sheer size and natural resources, could become powerful. "History is repeating itself," he says. "A century ago, the world needed rubber for tyres and 10 million people died in King Leopold's plantations. Now it wants coltan ore for the microchips of phones and gadgets, and Congo is home to 70% of reserves."

On his white coat, a badge given to Mukwege by a Jewish organisation cries for an end to the cynicism: "Don't stand idly by," it says. At Panzi, the message seems to have filtered down to all. "The other morning there was a rumour that my house had been attacked. When I arrived at the hospital, I saw three handicapped girls whom I knew because they are patients, waiting for me.

"The teenagers started hugging me and saying they had heard that my life was in danger. They explained that they had come to defend me. I had tears in my eyes. These handicapped girls wanted to help me, a big burly man. This is what I feel all the time from those who come to the hospital – the desire to keep loving, to keep giving, even when someone has tried to strip you of all your dignity and values. You cannot abandon people like that."