As I step off the train at Heysel, in the shadow of the notorious football stadium, the vast art deco structure of the Palais du Centenaire rises like a cathedral. With its four soaring buttresses topped by statues, the Palais forms the centrepiece of the Parc des Expositions in Brussels - a trade-fair complex built in the 1930s to commemorate a century of independence from the Netherlands. This is the temporary home of thousands of fish products from around the world as 23,000 delegates descend from 80 countries for the annual European Seafood Exposition - the world's largest seafood trade show and a grim reminder of man's dominion over the oceans.

"If I wanted people to understand the global fishing crisis, I would bring them here," says Sally Bailey, a marine programme officer with the World Wide Fund for Nature, one of the more moderate NGOs combating the exploitation of the seas. Last year, one of the more militant groups - Greenpeace - managed to "close down" five exhibitors trading in critically endangered bluefin tuna, by deploying 80 activists to drape their stands in fishing nets, chain themselves to fixtures and put up banners that read: "Time and tuna are running out".

Their main target was the Mitsubishi Corporation, the Japanese car manufacturer that is also the world's largest tuna trader, controlling 60% of the market and accounting for 40% of all bluefin tuna imported into Japan from the Mediterranean. The other companies were Dongwon Industries (Korea), Moon Marine (Taiwan/ Singapore), Azzopardi Fisheries (Malta) and Ricardo Fuentes & Sons (Spain).

The day I am there, Greenpeace activists are stalking EU fisheries ministers and waiting for a chance to unfurl their banners - but the security guards thwart them. However, the gargantuan catch on display speaks for itself. At the stand run by the Sea Wealth Frozen Food Company of Thailand, the shelves are groaning with jauntily designed packets of frozen squid, surimi (minced fish) dumplings, spring rolls, samosas and deep-fried cones with shrimp tails poking out of them. In the next aisle, a frenetic chef is wok-frying prawns from Madagascar, dipping them in little square dishes of cumin, coriander, chilli powder, salt, cinnamon and garlic. At the Taiwan Pavilion, the cabinets are full of chilled and frozen tilapia, barramundi, sushi, eel and vacuum packs of tobiko - orange flying-fish roe, salty, crunchy as granola and served by a young woman in national dress who literally has not heard of sustainability. "All the boats are out there catching fish with roe," she tells me. "With so many after the same species, this is a very difficult business for us."

These halls take several hours to negotiate, and the stands seemingly go on forever - 1,650 businesses in all, together peddling most of the 147m tonnes of seafood produced globally every year. Of this, 100m tonnes is caught in the wild while the rest is farmed to satisfy an insatiable demand. Already, 1.2bn people depend on fish in their diet - and in Europe we each consume 20kg per year on average, compared to 5kg per person in India. However, as the emergent middle classes in Asia develop a taste, and a budget, for seafood - considered a luxury item until now - demand will rocket further.

What the organisers must know, but are keeping mum about, is that the oceans are in a parlous state. The UN's Food and Agriculture Organisation estimates that 70% of the world's fisheries are now fully exploited (ie, fished to the point where they can only just replenish themselves), overexploited or depleted. The majority of fish populations have been reduced by 70-95%, depending on the species, compared to the level they would be at if there were no fishing at all. In other words, only five per cent of fish are left in some cases. In more practical terms, fishermen are catching one or two fish per 100 hooks, compared to 10 fish per 100 hooks where a stock is healthy and unexploited - a measure of sustainability once used by the Japanese fleet. In England and Wales, we are landing one fish for every 20 that we landed in 1889, when government records began, despite having larger vessels, more sophisticated technology and trawl nets so vast and all-consuming that they are capable of containing 12 Boeing 747 aircraft.

Where have all those other fish gone? In short, we have eaten them. "Tens of thousands of bluefin tuna used to be caught in the North Sea every year," says Callum Roberts, professor of marine conservation at the University of York. "Now, there are none. Once, there were millions of skate - huge common skate, white skate, long-nosed skate - being landed from seas around the UK. The common skate is virtually extinct, the angel shark has gone. We have lost our marine megafauna as a consequence of exploitation."

Then there are the devastating effects of bottom trawling around our coasts, which began with the advent of the steam trawler 130 years ago. "Sweeping backwards and forwards across the seabed, they removed a whole carpet of invertebrates," Professor Roberts says, "such as corals, sponges, sea fans and seaweeds. On one map, dating from 1883, there is a huge area of the North Sea roughly the size of Wales, marked 'Oyster beds'. The last oysters were fished there commercially in the 1930s; the last live oyster was taken in the 1970s. We have altered the marine environment in a spectacular way."

Worse still, after stripping our own seas bare, we have "exported fishing capacity to the waters of developing countries", Professor Roberts warns. Off Mauritania, Senegal and other West African countries, fleets from the rich industrial north are "fishing in a totally unsustainable way with minimal oversight by European countries". In return for plundering the oceans, which deprives local people of food, and artisanal fishermen of their livelihood, these vessels pay minimal fees that impoverished countries are happy to accept. "It is a mining operation," Professor Roberts says, "a rerun of the exploitation of terrestrial wealth that happened in colonial days. This is colonialism in a new guise, albeit with a respectable cloak in the form of access agreements."

Such is the human feeding frenzy, there may come a time when there are no fish left to catch. In 2006, a study in the US journal Science warned that every single species we exploit would have collapsed by 2048 if populations continued to decline as they had since the 1950s. By 2003, nearly a third of all species had collapsed, the study found - meaning their numbers were down 90% or more on historic maximum catch levels. Extrapolate that on a graph, and the downward curve reaches 100% just before 2050.

That prognosis - now disputed - was based on a four-year study of fish populations, catch records and ocean ecosystems. "We really see the end of the line now," said the author Boris Worm of Dalhousie University in Halifax, Nova Scotia, at the time. "It will be in our lifetime. Our children will see a world without seafood, if we do not change things." Many imagined a world where there would be no fish protein left to eat apart from jellyfish and marine algae.

What the study did not make sufficiently clear was that some fish populations had bounced back as a result of drastic measures by the authorities. In countries such as Iceland, Norway, the United States, New Zealand and Australia, fisheries management has been strengthened by controls that limit fishing effort (the number of boats out there, the time they spend at sea and the areas where they are allowed to fish). Another management approach, especially in Europe, is to control output (the amount of fish landed) using Total Allowable Catch quotas, or TACs. These are designed to maintain a stock's biomass - the estimated weight of fish left in the sea after fishing and natural deaths are taken into account. It should never be allowed to fall so low that a species is unable to spawn a healthy generation the following year.

Drawn up by scientists and organisations such as Ices (the International Council for the Exploration of the Sea), these quotas are discussed by fisheries ministers and fishermen at forums such as the EU. Both have vested interests, whether political or commercial. "If you put the fox in charge of the henhouse," Professor Roberts says, "decisions will be based on short-term constraints, such as paying the mortgage on the boat. Politicians, too, make choices that are beneficial to them or their constituents in the short term."

In other words, such gatherings often ride roughshod over the scientists' recommendations - as happened at a meeting of ICCAT (the International Commission for the Conservation of Atlantic Tunas) in Luxembourg in 2007, where quotas were being thrashed out for bluefin tuna from the Mediterranean. Scientists recommended an annual catch of 15,000 tonnes a year, with a preference for 10,000 tonnes - but EU ministers agreed a quota of 29,000 tonnes, enough to guarantee the collapse of the species. (Last year, quotas for 2009 were again set far higher than scientists were advising.)

In fact, the real amount of bluefin landed was 61,000 tonnes - four times what scientists had recommended - due to illegal and unreported fishing. Last month, the European Commission implemented a two-year control and inspection programme for bluefin tuna fisheries in seven Mediterranean countries, to clamp down on things such as illegal spotter planes used to track down tuna schools. Globally, black-market fishing is worth US$25bn (£17bn) a year. In Europe, 50% of the cod we eat has been caught illegally.

Those figures, and the Luxembourg debacle, are recorded in The End of the Line - the documentary, based on Charles Clover's book of that name, to be screened in UK cinemas from 8 June. However, the blatant disregard for science it portrays is not an isolated case. "We have analysed the decision-making of European fisheries ministers over the past 20 years," says Professor Roberts, "and systematically, year on year, they have set quotas that are 25 to 35% higher than the levels recommended by scientists."

How can our politicians get away with it? "There is no obligation upon them to take scientific advice," Professor Roberts explains. "What they will tell you is that it is only one of the things they have to consider. While they might be protecting a fisherman's livelihood in the term of one or two years, short-term decision-making like that guarantees stock collapse. It is not just a possibility, it is a certainty. The only uncertainty is how long it will take."

According to Professor Roberts: "What politicians should be deciding is how the catch is allocated within different nations. That is politics. What they shouldn't be deciding is how big the catch should be in the first place. That is science."

In Norway and the US, "they respect the advice of scientists", he adds - the best example being New England, where stocks of ground fish were in serious decline in the mid-1990s, but enlightened management brought them back. "At Georges Bank, they created a closed area of 20,000 square kilometres that was off-limits to mobile fishing gear [such as trawl nets]," Professor Roberts explains. They also cut fishing effort by a draconian 50% - putting many fishermen out of business. In the past 10 years, however, there has been "a spectacular recovery" of key economic species, Roberts says. "The haddock has bounced back, the flounder has bounced back, the scallops have bounced back, so it has been a great success story."

What this demonstrates is that, where there is political will, the tide can be turned on overfishing. In the US, a piece of 1976 legislation called the Magnuson-Stevens Fishery Conservation and Management Act has recently been reauthorised, requiring the industry to end overfishing in all federal waters by 2011. There is no such legislation in Europe. Under the existing Act, fisheries in Alaska and the North Pacific are already well managed - which is why wild Pacific salmon, Pacific cod and pollock from Alaska were prime candidates for certification by the Marine Stewardship Council (MSC), the international NGO that created a standard for sustainable fisheries in the late 1990s and upholds it. Why do these US fisheries tick all the boxes?

"They have very progressive management under the North Pacific Fishery Management Council," Professor Roberts says, "with precautionary targets - so they go for a relatively low fraction of the fish population each year. They have closures to protect habitats and valued species such as Steller sea lions and sea otters [which can get caught in fishing gear] plus extensive areas that are closed to protect deep-water corals from destruction by bottom trawling."The authorities also impose quotas for bycatch - other species caught by mistake - to protect them from exploitation.

These are the kinds of issues the MSC is looking at when certifying fisheries. So far, 43 have been certified, including 10 in Britain, while more than 100 are under assessment - but what exactly does that mean? "Right from the start, the idea was that fisheries would be independently assessed by a third party," says James Simpson, communications officer at the MSC, "so although we set the standard, we don't carry out the assessments. That is important, because it means we don't have any influence over the results."

Instead, marine scientists from certifying bodies such as Food Certification International and Moody Marine do the work, delving into every aspect of sustainability and producing a report up to 900 pages long. "They look at stock levels, based on historical records," says Simpson, "at the impact fishing is having on the environment and at the management plan for the fishery."

A score of 80 or more must be achieved against each of these three criteria for a fishery to be certified.

The initial assessment is peer-reviewed by fellow scientists, stakeholders such as environmental groups have their say - and the fishery gets to carry the eco-label on its products. "To do that, you have to be able to trace the fish all the way through the supply chain," says Simpson, "because you don't want any non-certified species or illegally caught fish slipping into an MSC batch."

The science may be rigorous, but will the MSC label change the world?

With some species, the label is making a big difference: 42% of the world's wild salmon catch is MSC-certified, and 40% of its prime white fish catch. Altogether, five million tonnes of seafood are certified by the MSC every year.

However, that is just five per cent of the wild-caught seafood market, which is why Professor Roberts believes the label itself "can only change a small number of well-informed people who actually care". The big effect, he says, is that supermarkets "have taken on board what the MSC is saying and have developed better fish sourcing policies of their own. They are the ones who can buy or not buy from a particular supplier, so they have a lot of power."

Sainsbury's - the largest retailer of MSC-certified seafood in the UK - has pledged that, by the end of 2010, it will source 80% of its seafood from MSC-certified fisheries or from the "green list" of species approved by the Marine Conservation Society. Marks & Spencer has promised that, by 2012, all its seafood will be either MSC-certified or from other independently certified fisheries. In May, it will launch a new range of prepared meals for outdoor eating and barbecues, based around gurnard, John Dory and black bream. Caught in season in British waters, these are a more sustainable choice than the "Big Five" overfished species - the cod, haddock, prawns, tuna and plaice that account for 80% of all seafood sold in Britain. If we take the pressure off these overexploited stocks, they will hopefully recover.

However, the MSC programme is about far more than shopping. In Europe, the growing number of certified fisheries has transformed the mood of EU fishing negotiations. The Dutch based Pelagic Freezer-Trawler Association (PFA) was the first North Sea herring fishery to be MSC-certified in May 2006, and the Swedish, Danish and Scottish herring fleets followed. Their representatives meet regularly in Brussels to talk about fisheries management. "All the major herring players in Europe are MSC-certified or under assessment," says Gerard van Balsfoort, president of the PFA, "and this has led to a certain kind of behaviour in the advisory process. From the point of view of stocks, you can't just ask for a higher quota if it isn't scientifically based. You can't just shout for what you want. "

In the seas around South Georgia - a remote Overseas Territory of the United Kingdom 1,300km from the Falkland Islands - the Patagonian toothfish fishery was required by MSC certifiers to initiate research that would locate deep-coral areas vulnerable to damage by trawl gear. If such areas were found, efforts to protect them "should be considered", the certifiers said. In fact, the fishery went further. It identified three deep-coral areas that needed protecting and closed them to fishing vessels entirely. That way, fish and fragile habitats would have a chance to recover.

In South Africa and New Zealand, too, MSC-certified fisheries (for hake and hoki respectively) have helped create Marine Protected Areas (MPAs) where trawling is banned, either by funding research or by lobbying the government. In New Zealand, 30% of the Exclusive Economic Zone - an area extending 220 miles out to sea over which it has rights - has been closed with fishing industry approval.

Such closures could provide the answer to the fishing crisis, allowing our children and our grandchildren to eat fish with a clear conscience. In Iceland, Canada and the US, the creation of MPAs "has brought real increases in fish populations and real recovery of seabed habitats", Professor Roberts reports. "Populations of exploited species have increased five-, 10- or even 20-fold within five, 10 or 20 years," he says. "What you see is the flourishing of life."

Over time, this explosion of fecundity spreads to other parts of the ocean. "The benefits of protection flow to the surrounding fishing grounds through the emigration of animals from protected areas, and the export of their offspring on ocean currents," Professor Roberts says. "The eggs and larvae of these protected animals are transported to fishing grounds and can replenish them."

In his view, 30% of the world's oceans should be protected "to set the clock back 200 years" and reverse the fishing crisis. After that, responsible fisheries management "in the North Pacific mould" could avert the 2048 scenario. The trouble is, only 0.8% of the oceans are currently closed to fishing - despite the efforts of former President George W Bush, who "single-handedly created MPAs, dotted throughout the Pacific Ocean, which now constitute 31% of all MPAs worldwide", Professor Roberts says.

In Britain, too, MPAs are seen as part of the solution. The Marine Bill is grinding its way through Parliament, with a provision to create MPAs in territorial waters up to 12 nautical miles from our coast. Britain and Europe have pledged to create networks of MPAs by 2012.

Far from campaigning for a total ban on fishing, Professor Roberts believes it should be allowed. If properly regulated, it will increase global fish production rather than decimate it. "Fisheries science suggests that a species is healthiest when you reduce its population size by 50%," he says. "That way, you remove the larger, older, slower-growing animals and the population becomes dominated by smaller, faster-growing fish. For them, the availability of food increases and they thrive. That gives you a boost in population growth rate, which gives you a higher rate of production to exploit."

Perversely, fishing could swamp the world with fish protein rather than starve it - but it has to be done differently. "We should abandon quotas," Professor Roberts believes, limiting fishing effort rather than output. "If you're not out there catching fish, they're not going to die." At present, EU vessels that exceed their quota have to dump fish overboard dead, rather than land it illegally. "You've got one or two times as many fish being killed and discarded, sometimes, as are being landed," Professor Roberts says. "That is no way to manage a fishery; that is not sensible at all. You have to land all your catch."

Reforms such as this will require "a major change of political direction on this side of the Atlantic", Professor Roberts warns - "but if we have that, we can turn back the clock within 20 years, to the point where a lot of species are in a far more productive state. None of this is rocket science. Perhaps we need good old George W Bush back... the world's greatest marine conservationist!"

• Read more from Andrew Purvis about fish on OFM's food blog, Word of Mouth. Go to www.observer.co.uk/foodblog. The End of the Line will be released in June