People say the internet is changing the world, but I'll tell you this: aquaculture is going to be far more important to far more people.' It is nearly 50 years since Hagen Stehr arrived in Australia to earn a living as a tuna fisherman, but his gruff German accent is still strong. 'Look at agriculture - we're running out of land, we're running out of water. Look how the prices of food are going up. In the future, people's protein is going to have to come out of the sea - it's all we have left.'

If money talks, then Stehr deserves to be taken seriously. Every Thursday he and his fishing friends meet in a café in Port Lincoln, the small fishing community near Adelaide on Australia's south coast that they have made the country's richest town. When the four members of Stehr's 'Cappuccino Club' gather, he says, there's more than a billion Australian dollars (nearly half a billion pounds) at the café table.

They made the money from killing and selling bluefin tuna. A single one of these beasts can cost as much as a Volvo (in January a 276kg bluefin sold for £28,000 in Tokyo) because its belly meat provides the sweetest sashimi of all. The bluefin is, as a result, one of the world's most endangered food animals - not that that's stopping the fishing. Stehr and his friends, who own the majority of Australia's tuna fishing licences, made their first fortunes catching tuna in the normal way, by hook and net. But in the early Nineties, worried by ever tighter quotas on the disappearing bluefins, the Cappuccino Club pioneered the 'ranching' of the fish.

This was one of the most brilliant ideas in the history of industrial fishing, and it has now spread all over the world. What Stehr and his friends do is catch young bluefin. Since quotas limit the tonnage of fish caught, this allows them to take more. They then corral them in vast purse-shaped nets that are hauled by tugboat around the southern ocean at less than one mile an hour for eight months. The ranchers, marine cowboys, battle storms and fend off sharks, and all the time they feed the growing tuna.

Ranching tuna is, of course, bonkers: one of the most scarily inefficient and unsustainable factory farming methods known to mankind. For a start, it can take up to 25 kilos of feed fish - sardine and pilchard is the captive bluefin's preferred diet - to produce one extra kilo of tuna. But that kilo of bluefin can sell for £100 wholesale, and during those months in their sea-borne fat-farm the tuna double in size.

From his house above Arno Bay outside Port Lincoln, Stehr can enjoy a fine view of the ocean where his tuna are ranched like cattle on the plains. He can also see his fleet of 22 support vessels and the array of laboratories and holding tanks built for his new big idea. This is even more revolutionary. 'Seven or eight years ago I was watching the fish in the ocean rings, I was worrying about the quotas (Australia and Japan are both allowed to catch between 5,000 and 6,000 tonnes of southern bluefin a year) and I thought - hey, what about we breed them?'

At least £15 million later Stehr says he is almost there. 'We've been up the north-east face and the glaciers. Now we're on the Hillary Step and I can see the top of Everest.' His scientists have controlled the sunshine, mimicked the temperature and the oxygen content of the waters from the Antarctic to the southern Indian Ocean through which the fish migrate. They've persuaded the male bluefins to produce sperm and, with added hormones, they've coaxed the females to grow eggs. Soon they will anaesthetise the female fish and strip out the eggs for fertilisation.

'We've closed the life cycle of the fish. It's now not a question of if, but when we produce young. It could even be in the next couple of weeks,' he told me this month. Stehr knows that Japanese companies are after the secrets of his breeding techniques, so his facilities are surrounded by 24-hour guards and barbed wire. 'It's like Stalag Luft 13', he laughs.

There are those who doubt that Hagen Stehr can lay his hands on what all fish farmers agree is the industry's Holy Grail. But his company CleanSeas has already managed to breed and establish a commercial market for another tuna-like predator fish, the kingfish. Waitrose is expected to start stocking it this year.

Think farmed fish, and you'll probably picture cheap salmon chunks with an oily orange hue and dubious flavour. But farmed fish is increasingly varied, and increasingly impressive in quality - in a well-stocked supermarket now you can find farmed trout, sea bass, bream, turbot, cod, halibut, mussels, scallops, crayfish, tropical prawn and mud-crab as well as exotic new breeds like catfish, tilapia, carp and barramundi (funny how the celebrity chefs are pushing those, isn't it?). They're farmed in pens and tanks, and, around the equator, in muddy ponds made from flooded rice paddies and former mangrove swamps. Farmed cod, under the No Catch brand, comes from the Shetland firm Johnson Sea Farms, and it's considerably better than the wild fish - and considerably more expensive. At the moment, shops have no duty to tell you if your fish is farmed - but if it's salmon, sea bass or tiger prawns, you can be pretty sure it never saw the wide blue seas.

You had better get used to eating fish from cages. By 2010, half of all the fish and sea-vegetables the world eats will be farmed, according to the UN Food and Agriculture Organisation. Much of that will be in Asia, especially China, where fish consumption has doubled in 15 years - they now eat more in kilos per head than the British. Both technology and demand are speeding up the shift. With many wild stocks in steep decline, and most international agreements to conserve them proven as useless as a straight fish hook, farmed fish may in a few decades be the only way anyone but the very rich can get their Omega-3.

So what's wrong with that? The one great global resource - as Hagen Stehr points out - that humanity has not pushed to the point of exhaustion is the sea. But we're running that one down - last year the journal Science predicted that, at current rates, 90 per cent of the world's fisheries will be finished before this century is half gone. It may well be that if we change our habits to eat farmed fish, rather than beef or chicken, we will avert the crisis in global food supply that every authority says faces us in the 21st century. Thousands of years ago human beings domesticated cattle and pigs to use them more efficiently - why not fish? Could aquaculture not only save the bluefin tuna from extinction, but feed the world too?

If only things were so simple. At the World Seafood Summit - a gathering of fish industry bosses, fishermen, retailers and green groups in Barcelona this January - I saw the early tremors of what may turn out to be an upheaval of international protest against fish farming. At a packed side-meeting Greenpeace unveiled a long-awaited report, 'Challenging the aquaculture industry on sustainability'. There was a frisson in the crowd as the presentation kicked off with a photo of a graffiti made of buoys that spelt out 'No fish farms' beside a salmon fishing pen in a Chilean fjord. In the water bobbed crucifixes to denote farmers and local fishermen bullied out of their rights to accommodate industrial aquaculture.

Greenpeace's Nina Thuellen, head of seafood markets, was at pains to stress that the organisation was not against all fish farming. 'So long as it's done in a sustainable manner. There is a need for aquaculture where fish is a key protein for people.' It was quickly pointed out to her that, essentially, this meant the organisation was against any fish farming for or in the rich world (because fish is not crucial to our protein source) and against farming of salmon, trout, cod and indeed any fish that has to be fed on other fish, because of its inefficiencies.

'The feeding of fish to fish in order to feed humans can never be sustainable,' said one audience member, and the Greenpeace scientific researcher Cat Dorey nodded. It was hard to disagree - salmon need three kilos of fish to produce a one kilo weight gain, and all too often they are fed on fish-derived oils or fish - like sand eels - that are crucial to sea birds and other fish. Another major issue is the greenhouse gas emitted by fish farming, the production of feed meal and the transport of the fish to the customer. Projects like the farming of tropical fish in the northern hemisphere - there's a barramundi farm in the New Forest - demand massive resources in heat as well.

There were grumbles in Barcelona at Greenpeace's rigid laying down of the law. One salmon-farming insider called it 'kindergarten stuff'. But bodies that try to straddle the concerns of industry and consumers, like the Soil Association, are more pragmatic. It is driven primarily by the perception that fish farming is here to stay. 'Aquaculture is increasingly going to supply the world's fish needs - we have to accept that, and work to make it sustainable,' says the director of the Association's Scottish arm, Hugh Raven. He was key in the organisation's controversial move two years ago into certifying salmon farms as organic.

This was done to the furious disapproval of some of the Association's more fundamentalist supporters, who say that such an unnatural way of treating a wild animal can never be in accord with the tenets of the organic movement. And there is indeed a price to pay for all fish farming. Escaped farmed fish harm wild stock, and can contaminate them with a variety of ugly diseases that they develop from being kept in such unnatural and close confinement. (I've got a spectacularly horrible picture of the nodules that farmed cod in Norway have been developing on their eyes and other organs.)

A major objection comes from the Americans - where, legally, organic farmed salmon is an impossibility. The US authorities understandably insist that the water in which the fish swim and everything they ingest cannot be guaranteed to be organic. (To US producers' annoyance, Scottish organic salmon farmers have thus found a lucrative new market in the States.) Other issues that are exciting the campaigners include the environmental abuse that fish farming, with its chemicals and toxic run-offs, can do to their neighbourhoods.

Weathering this storm, the Soil Association is now insisting that by 2010 all its certified fish farms feed 100 per cent sustainable fish to their salmon, either as off-cuts from fish processing, or as fish certified as sustainable by the Marine Stewardship Council (MSC). This is the non-profit making body, whose blue tick logo is used by Tesco, M&S, Sainsbury's and fish suppliers in 35 countries to brand fish as sustainably caught. But here as MSC chief executive Rupert Howes told me, there is a problem. 'We assess fisheries on the scientific evidence of sustainability. We don't enter the ethical debate around what that fish is used for.' And the morality of feed-fish is currently a big, thorny problem.

In the Chilean fish-farms marked out by Greenpeace, the salmon - destined for tables in North America - are fed sardines or anchovies, fish humans could very happily eat. The MSC has certified the Mexican sardine fishery as worthy of its blue tick - even though most of its production will go to fish farms. Meanwhile, the tuna of Australian ranches eat pilchard caught off the shores of West Africa. This is what Charles Clover, the environmental journalist and author of an influential book on the decline of fish, The End of the Line, calls an 'obscenity on an Imperial Roman scale...the diversion of low-value fish from the mouths of people in developing countries into the mouths of well-fed fish in the developed world'.

Another fish-farm sceptic at the Summit was Professor Callum Roberts, who has recently published a fascinating survey of marine exploitation over the years, The Unnatural History of the Sea. He states that the destruction of 50 per cent of the world's coastal mangrove forest in recent years is due, in part, to make way for tropical fish farming - that's those 'fresh' tiger prawns from Ecuador or Thailand you can buy in all supermarkets. From Bangladesh to Indonesia, the loss of mangrove, which should protect low coastlines and the people who live there, has been directly linked to the rising annual death tolls in tropical storms, and indeed some of the hundreds of thousands of deaths in the 2005 tsunami.

Not all good, then, fish farming. So will we soon see celebrity chefs weeping over caged fish, as is now fashionable with battery chicks? One of the first to shed a tear would be the Michelin-starred Tom Aikens, not known in the catering trade as a softie, but a true militant on the subject of fish stocks and sustainability. Aikens was at the Barcelona Summit to talk about his new restaurant, a fish and chip shop called Tom's Place, which opened this month in west London. At Tom's Place there will be no farmed fish - everything will be wild, and sustainably caught. And a piece of cod in batter will start at £12, scampi at £20.

'There's a strong case both for and against farmed fish. But I don't use it. I just don't think it tastes like the real McCoy,' he told me in Barcelona. 'And I think feeding wild fish like sand eel and whiting to the farmed ones, at a 6:1 ratio, in terms of producing weight, is just morally wrong.

'We're clearly getting things wrong with mass farming on land - Mother Nature told us that: we got foot and mouth, we got mad cow disease. What's going to happen in aquaculture? What I'd like to see is standards, accreditation, and so on, so as farmed fish grows, the public can understand properly what they're getting.'

Aikens is not alone. Nigel Edwards of the Grimsby processing firm SeaChill was just one of many pleading in Barcelona for the NGOs and lobby groups to get their act together, to end the 'logofest' of competing labels that judge, from a vast number of viewpoints, whether a fish farm or aquaculture method is good or bad. Melanie Sachdeva, fish and poultry manager of Tesco said, 'Customers are just not going to pay a premium for sustainable fish until they understand it better'. The danger is that the huge growth of the market in 'sustainable' fish and the lack of a universal standard - as there is for organic and fairtrade - will just confuse the punters more.

But at the Summit no one seemed to be anywhere near getting this crucial gap plugged. The MSC, according to Rupert Howes, has decided to concentrate its efforts on certifying the feed-fish for aquaculture, not fish farms themselves. Instead, some outfits that are trying to go it alone - like the Italy-based Friends of the Sea, were denounced as 'unscientific' at the Summit. And so you can only imagine, as WWF's Meredith Lopuch warns, that without standards the industry will race on towards producing the cheapest fish possible.

Marks & Spencer's fish expert, Andrew Mallison, told the Summit of a visit to a supplier, a tilapia farmer who lived just up road from a massive battery chicken operation. The farmer asked him, 'What's to stop me feeding the chicken off-cuts to my salmon?'. 'I wouldn't want to tell a customer that there's chicken parts in his fish,' said Mallinson, and everyone nodded and laughed. But they all know the answer to the fish farmer's question - there's nothing to stop him feeding chicken guts and ground-up feet or anything else he likes to the fish in his cages.

'It's a young industry, and mistakes have been made,' says Mallison. There are organisations that are trying to right these - the World Wildlife Fund sees aquaculture as so important an issue for the environment that it is putting serious money into working out aquaculture standards that they hope will become global. These will not be ready for at least another year, however.

The Soil Association is tightening its 'organic' standards for fish farming, and has despatched a team to inspect Hagen Stehr's operation in Australia. There are high hopes of new, non-fish feeds for aquaculture - the use of algae or ragworms. Krill and other micro-organisms still abundant in the ocean are another answer. Even Hagen Stehr, through the use of cereals and canola oil, claims he has reduced his fish-to-tuna kilo ratio from 1:25 to 1:3. But this feed is not, of course, 'natural'.

'There's those who say that the best solution to these problems, and particularly the ecological footprint of fish production, is to restore the seas to their natural fecundity. I agree, but that's a long way away. And aquaculture may play its part in bringing that about,' says the Soil Association's Hugh Raven, who is also a member of the Government's Sustainability Commission. 'In any case aquaculture will surpass wild capture fisheries soon. We need to make it sustainable - and I think the most challenging issue is dealing with the greenhouse gas emissions.' While supporting salmon aquaculture, Raven does agree that the central moral problem of carnivorous fish farming must be addressed - 'I do think we must move to where the feed is a waste product - like off-cuts of other fish - than the product of a food fishery.'

So what does a fish-loving fish-eater do? Buy vegetarian or omnivore fish, of course. Bottom-feeders like carp convert their fish food - which no human would ever want to eat - into weight gain just about at a one-to-one ratio. They're pretty close to sustainable, and Jamie Oliver has recipes for them. The problem is, they're just not tuna.