Anti-whaling activists threw paint and foul smelling acid at a whaling ship in the Antarctic ocean Saturday in a fresh bid to halt the annual hunt, officials said.

Two boats belonging to the US-based environmental group Sea Shepherd approached the Japanese whaling vessel Yushin Maru No. 2 (YS2) and launched 40 bottles containing paint and butyric acid, Japan's Fisheries Agency said.

"YS2 gave warnings, by voice and water cannon, to the obstructive activities," the agency said in a press release, adding that the ship also floated buoys to deter the activists' boats.

None of the YS2 crew was injured but the ship's hull was smeared with the targeted acid and paint.

The agency called Sea Shepherd's actions "extremely dangerous acts which threaten the safety of our country's vessels and the life of its crew".

The Sea Shepherd launched similar attacks against Japanese whaling fleet earlier this month.

Sea Shepherd said three of its members were injured when Japanese crewmen used grappling hooks and bamboo poles to deter them in a high seas clash on Wednesday.

On January 7, three activists from another environmental group Forest Rescue Australia boarded another whaling boat Shonan Maru.

Japan only agreed to hand the men over after intervention from Canberra, and they were returned to Australia later by a border protection vessel.

The Japanese whaling fleet, led by the 720-tonne Yushin Maru, was seen leaving the Japanese port of Shimonoseki on December 6 for the annual hunt, with security measures beefed up after clashes in previous years.

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.