Friday, 10.30pm, 61 degress South 120 West. Captain Paul Watson is on the bridge of the Steve Irwin, steaming due west at 17 knots in heavy seas past the ice floes of Wilkes Land in northern Antarctica.

Roughly 100 miles ahead of the former Scottish Environment Protection Agency patrol boat, now painted black and flying the jolly roger, is the bulk of the Japanese whaling fleet – mother ship, four harpoon hunter vessels and a security patrol boat – with a licence to kill 935 minke, 50 fin and 50 humpback whales in the next few weeks. Behind the Irwin, near the French Antarctic base of Dumont d'Urville, is the Bob Barker, Watson's second ship. It in turn is being pursued by a second Japanese security ship. Meanwhile, at the bottom of the Southern Ocean is the Ady Gil, the third ship in Captain Watson's anti-whaling navy. The $2.5m space-age catamaran-style, biofuel-powered, ocean-going speedboat sank on Friday morning after being hit by the Shonan Maru 2, one of the Japanese whalers.

"Not hit. Deliberately rammed," corrects Watson, at 59 still the world's least compromising and most romantic environmentalist. On a satellite link he says: "The Gil was almost stationary in the water. [The Shonan Maru 2] changed course abruptly and steered straight into it. One crewman broke two ribs. It was a miracle that no one was killed."

I had travelled with Watson and the Sea Shepherd Conservation Society from Scotland to the Faroe islands in 1999. Watson was even then a notorious figure, not unlike Captain Nemo, the Jules Verne character who roamed the depths of the sea in his submarine, the Nautilus.

"Nemo understood that it did not matter what humans thought, because humanity was the problem. His duty was to save life in the sea from the greed of mankind. I understand that philosophy and I have lived it every day of my adult life," he said.

Back in 1999, his crew of young volunteers were disciplined and clearly in awe of their captain, who accepted no "consensus shit", "abided no drugs" or "friggin' in the riggin'", and who forbade meat-eating aboard his ship. Few had been on a boat before, but everyone had complete confidence in his skills as a mariner and his respect for, and command of, international maritime law. They also expected and hoped for peaceful confrontation and seemed prepared to go to whatever lengths Watson asked of them.

We hunted whalers night and day for a week, but found none. Instead we were buzzed by the Danish air force, boarded by customs officers and ordered by the police to keep away from the islands. When I eventually asked to be put ashore to talk to the Faroese, Watson willingly provided an inflatable and dropped me at midnight on a beach. I was arrested and then imprisoned for illegal entry within minutes. Sea Shepherd clearly has the power to scare communities by doing nothing at all.

Last week Watson was full of praise for the 77 people from 16 countries, including Japan, who are crewing his three ships this year. In 30 years of harassing industrial fishers, he has taken 4,000 volunteers to Antarctica, the Pacific and the Atlantic to try to stop whaling, sealing and illegal fishing. Few have returned anything other than inspired and committed.

The sinking of the Gil was just the latest skirmish in what has become an annual battle between the volunteers for the California-based Sea Shepherd Conservation Society, which Captain Watson founded after leaving Greenpeace in the 1970s, and the Japanese Institute of Cetacean Research, a scientific research body that has effectively become the Japanese government's whalers.

For the last nine years these two small navies have clashed dramatically in the Southern Ocean Whale Sanctuary, an area of 50 million square kilometres (19 million square miles) in which the International Whaling Commission (IWC) has banned all types of commercial whaling.

One year the whaling fleet was chased 3,000km (1,850 miles) through icebergs; another, two Sea Shepherd volunteers were captured and tied to the railings of a Japanese ship after they had been invited on board; three years ago the Japanese allegedly shot at Watson; there have been water cannon battles, and last year the Japanese escalated the war by throwing concussion grenades on the Sea Shepherd boats. Sea Shepherd responded by throwing bottles filled with non-toxic but foul-smelling butyric acid on the Japanese. Each year the accusations have flown and the language has become more colourful: "We are obsessed with stopping the cetacean Death Star, that vicious, cruel killing machine and her fleet of boats armed with explosive harpoons," says Watson.

But what precisely happened last week is still not clear. It has been the subject of official protests by both vessels, and will be investigated by the Australian and Japanese governments, and possibly one or more courts. From videos released by both Watson and the Japanese in the last 48 hours, it appears that the Shonan Maru 2 bore down on the Gil with its water cannon blasting and issuing warnings from its loudspeaker that it had "authority to repel". No one disputes that it then sliced through the bow of the Gil, scattering its crew of six.

The Japanese accuse Sea Shepherd of being "hostile eco-terrorists". "The Sea Shepherd extremism is becoming more violent. Their actions are nothing but felonious behaviour. Aiming directly to the Nisshin Maru crew, the activists have repeatedly fired illegal high-powered laser devices that can produce blindness when irradiated to the naked eye and have fired projectiles containing butyric acid, a substance highly hazardous to the human body including skin and eyes," said a spokesman for the institute.

Yesterday lawyers working on behalf of Sea Shepherd lodged papers in a Dutch court accusing the Japanese of "piracy and violence". They in turn dismissed his statements as lies and accused Sea Shepherd of pollution and using bows and arrows.

But the private war has become more public and visible thanks to the internet, and the "whale wars" now threaten diplomatic relations between Australia and New Zealand and Japan. Both antipodean countries are officially embarrassed by the incidents taking place, but have a public overwhelmingly on Watson's side.

This year the Japanese fleet's position was relayed to Sea Shepherd not unofficially by the Australian navy, as it has been in the past, but first by small boats near Tasmania, and then by outraged holidaymakers aboard the cruise ship Orion, which happened on the whaling fleet as it was refuelling.

Watson is adamant that he is no terrorist. "In 31 years harassing and confronting whalers, sealers and illegal fishers, we have never injured a single person, never been convicted of a felony, or been sued. Sea Shepherd does not condone, nor do we practise, violence," he says. "We agree with the assessment by Martin Luther King that violence cannot be committed against a non-sentient object. Sea Shepherd sometimes damages equipment used for illegal activities, but we have an unblemished record."

"We think [the Japanese] are re-enacting the Second World War," said Watson yesterday. "They see themselves as against the West and that no one will tell them what to do."

But he freely admits damaging property. In a lifetime of confrontations beginning with Canadian sealers, he has used "prop foulers" to sabotage ships, boarded whaling vessels, and sunk several in Iceland and Norway.

"We're not a protest organisation. We intervene against illegal activities, and as far as we're concerned Japanese whalers are poachers. The oceans are being pillaged and we are the only organisation out on the high seas trying to do something about it," he says.

He told me he acted by a martial code culled from the methods of ancient eastern and modern western warfare, and that he expected to die for his cause. He quoted films, read widely, wrote poetry and books, laughed a lot.

Watson claims to have co-founded both Greenpeace and Greenpeace International in the early 1970s (something that Greenpeace disputes), but proved far too much for them. "He was a great warrior brother, yet in terms of the Greenpeace gestalt he seemed possessed by too powerful a drive, too unrelenting a desire to push himself front and centre, shouldering everyone else aside," said his friend Robert Hunter, who died four years ago.

He sailed with Greenpeace many times, and skippered one of its boats in 1972. But he severed all links with the organisation in 1977, after being expelled from the Greenpeace board.

What he wrote in his autobiography 16 years ago holds just as true today, he says: "There are many people who say that what we do is futile, that there is no way to stop the rising tide of human-spawned destruction. There are many who condemn my crew and I for taking the law into our own hands and for taking on the barons of corporate profit. There are some who would like to see us jailed or even dead, so blinded are they to the conceit and folly of their own anthropomorphism.

"I don't care. I do what I do because it is the right thing to do. I am a warrior and it is the way of the warrior to fight superior odds."

A life of protests



Nuclear weapons

In 1969 Paul Watson protested against Russian nuclear testing with the Don't Make a Wave committee, which later evolved into Greenpeace. He then tried to disrupt nuclear tests in the Pacific.

Seals

Watson has opposed the Canadian seal hunt since 1983. He blocked the port at St John's in Newfoundland, and brought the hunt to a near standstill. The hunt was later banned for 10 years after he took Brigitte Bardot to pose with a baby seal on the ice.

Whaling

Watson has outraged the governments of Japan, Iceland, Norway and Denmark by sinking or ramming whaling ships. He has chased the Japanese whaling fleets in Antarctica for nine years, claiming to have prevented the deaths of thousands of whales.

Fishing

Since 2000 Watson's ships have patrolled the Galápagos and Cocos Islands to try to stop illegal fishing, causing consternation among fishing fleets and governments.