The annual battle between Japanese whaling vessels and environmentalists in the waters around Antarctica is heating up yet again. But this time around, both sides are using more extreme methods to pursue their opposing aims. And with the governments involved also taking a harder line, the issue is threatening to affect wider security relationships in ways that are in nobody’s interest.

Commercial whaling was banned under a 1986 international treaty. But Japan, which considers whaling a cultural tradition, is allowed an annual ‘scientific’ hunt, saying it culls whales for research. The meat is sold on local markets.

Last month, Japan upped the ante by announcing that it intended to take New Zealand protester Peter Bethune to Japan for prosecution after he boarded a Japanese whaling vessel in Antarctic waters.

The announcement heralded a major policy change. Despite a 21-year history of bitter anti-whaling campaigns in the Antarctic, none of the protesters involved has ever been charged in Japan. When two activists boarded a Japanese whaler in 2008, they were held until an Australian fisheries patrol boat agreed to pick them up.

Boarding the Japanese vessel under cover of darkness, the New Zealander said he wanted to make a citizen’s arrest of the ship’s captain and hand him a US$3 million bill for the destruction last month of his protest ship, the Ady Gil. His real intention, however, was almost certainly to be detained aboard the whaler and thus turn the issue into an international incident. The Japanese took the bait.

Trespassing on a Japanese ship "is outrageously illegal behaviour", said Japanese fisheries minister Hirotaka Akamatsu. Reports say that Bethune is being held in a room by himself on the whaler and is under 24-hour guard pending transfer to Tokyo.

Apart from New Zealand, Australia has also been dragged into the controversy. This is because the collision between the Ady Gil and the whaling fleet’s security ship, Shonan Maru No.2, took place inside waters declared by Canberra to be a whale sanctuary. Australia opposes the Japanese whale hunt, but it has avoided sending patrols into the area this year. Japan has been one of Australia’s most important trading partners for decades. The two countries signed a defence pact last year, and are currently in talks on a free trade agreement.

Just what Tokyo expects to gain from prosecuting Bethune is not clear. Indeed, its harder line could play into the hands of the conservationists by giving their cause greater publicity. It has already forced the Australian government to state its position on whaling more strongly. Last month, Australia vowed to take Japan to the International Court of Justice if it did not stop whale hunting in the Antarctic.

Several MPs from the ruling Democratic Party of Japan have called for Japan to respond by suspending negotiations with Canberra on a proposed joint military logistics agreement. But this would hardly be in Japan’s interest. The agreement creates a framework for the two militaries to provide each other food, fuel and other logistical support during peacekeeping operations and disaster-relief missions. In effect, it allows Japan greater flexibility in projecting its influence beyond its own waters. The tightly constrained Japan Self Defence Force has only one other similar agreement, with the United States.

Up to now, whalers and conservationists have stopped short of using deadly force. In an attempt to stop the hunt, anti-whaling vessels have dangled rope in the water to try to snarl the propellers of Japanese ships. They have also hurled rancid butter ‘stink bombs’. The whalers have responded by firing water cannon and using military-style acoustic weapons designed to disorientate the activists.

But the mood is changing. Bethune has accused the crew of the Shonan Maru of ‘attempted murder’, claiming that his ship was deliberately rammed. And Japanese officials have begun referring to ‘acts of piracy’ allegedly perpetrated by conservationists. Since the sinking of the Ady Gil, there have been more collisions involving Japanese whaling ships and vessels belonging to the Washington-based Sea Shepherd Conservation Society. None, however, has been sunk.

Supported by popular opinion in Australia and New Zealand, Greenpeace and Sea Shepherd ships continue to base their operations in the ports of these countries. US television personality and animal rights activist Ady Gil has also said he is "very interested" in replacing the carbon fibre trimaran racing vessel named after him.

The conservationist cause has also been bolstered by a recent study by researchers at Oregon State University and Stanford University, which has undermined Japanese claims that the population of minke whales in the Southern Ocean was growing. Australia and New Zealand are also supported by the European Union and the US in international whaling forums.

Japan, it seems, has locked itself into a whaling war in the Southern Ocean that it cannot win.