A US judge has refused a request to stop the Sea Shepherd activist group from disrupting Japanese whalers.

Several Japanese whaling groups had been seeking a court order to prevent the Sea Shepherd group from "engaging in physical attacks" on their ships in the Southern Ocean.

"Over the past few years, defendants have engaged in repeated, relentless violent attacks against plaintiffs in the Southern Ocean," read the injunction request, filed in Seattle.

The whaling groups - including the Institute of Cetacean Research - said crew members were put in danger by the actions of Sea Shepherd, which it described as "essentially self-proclaimed pirates".

But a judge in the state of Washington, where Sea Shepherd is based, has rejected the request. A full judgement will be issued at a later stage.

Sea Shepherd activists have been involved in several clashes with Japanese whalers in recent months.

Founder Paul Watson says the group aims to save as many whales as possible.

Last month, Japan's Fisheries Agency said anti-whaling activists threw paint and foul-smelling acid at a whaling ship in the Antarctic ocean in a fresh bid to halt the annual hunt.

Two boats belonging to Sea Shepherd approached the Japanese whaling vessel Yushin Maru 2 and launched 40 bottles containing paint and butyric acid, the agency said.

That clash came one week after three activists from a different group were handed over to Australian authorities after boarding a Japanese boat.

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.

ABC/AFP