Anti-whaling activists have interrupted the Japanese Antarctic hunt for the first time this season, Japan's fisheries agency said Thursday.

Two small boats from the US-based environmental group Sea Shepherd interfered with the movement of the harpoon ship Yushin Maru 3 for five and a half hours in the Antarctic Ocean on Wednesday, the agency said.

The boats, lowered from the Sea Shepherd vessel Bob Barker, cut across the Yushin Maru's path trailing ropes and wires, an official at the governmental agency's international affairs division said.

"In response, the Yushin Maru 3 discharged water and gave out verbal warnings to the boats," he said, adding the whaler was not actively hunting at the time.

He refused to comment on the fleet's composition or the location of other vessels at the time.

Three whaling ships, led by the 720-tonne Yushin Maru, were seen leaving the Japanese port of Shimonoseki on December 6 for the annual hunt, with security measures beefed up amid simmering international protests.

In previous years, a mother ship has joined them later.

Their mission is officially said to be for "scientific research", with the fleet aiming to catch around 900 minke and fin whales, according to a plan submitted by the government to the International Whaling Commission.

In February last year, Japan cut short its hunt for the 2010-2011 season by one month after bagging only one fifth of its planned catch, blaming interference from Sea Shepherd.

Commercial whaling is banned under an international treaty but Japan has since 1987 used a loophole to carry out "lethal research" on the creatures in the name of science.

Japan has claimed it is necessary to substantiate its view that there is a robust whale population in the world. It makes no secret of the fact that whale meat from this research ends up on dinner tables and in restaurants.

The governments of the United States, Australia, New Zealand and the Netherlands jointly announced in early December they were "disappointed" over the start of the annual hunt.

Sea Shepherd confirmed its encounter with the Yushin Maru 3 on Wednesday.

It said the Bob Barker vessel found the harpoon ship some 200 nautical miles north of the French Antarctic base Dumont d'Urville.

"The Bob Barker has been out at sea for about four weeks and this is the first whaling ship we've come across," second mate Vincent Burke told AFP from the area, which he said was thick with ice.

Burke said his vessel had been searching for the Japanese factory ship the Nisshin Maru in the hope of preventing it from processing any whale meat when it came across the harpoon boat.

Sea Shepherd activists aim to harass the Japanese whalers each year during their hunt in the freezing waters off Antarctica and this time first located the Japanese fleet on December 25 with the help of a drone.

The unmanned plane, small enough to be launched by hand from the deck of the ship, is fitted with cameras and detection equipment.