Japanese whalers on Tuesday celebrated what they described as a court victory in the US to end years of high seas clashes with anti-whaling group Sea Shepherd, which immediately vowed to fight on.

The arch enemies have waged a legal and public relations battle as Sea Shepherd has sought to disrupt an annual whale hunt in the Antarctic that Japan defends as scientific research.

However, the settlement between the US-based Sea Shepherd Conservation Society and Japan's whaling body is unlikely to end the dispute as operations in Antarctic waters are mostly carried out by Sea Shepherd Australia, which does not come under the ruling.

On Tuesday, the Institute of Cetacean Research and Kyodo Senpaku -- key players in Japan's whaling industry -- announced a legal settlement that would bar the US group from attacking whaling ships or funding such activities.

The parties involved "successfully resolved the dispute through mediated negotiations earlier this month", it said.

But Sea Shepherd played down any suggestion of a global agreement, saying the settlement only applied to its US arm and that other branches, including its Australian office, would keep fighting.

"The ruling in the US courts affects ONLY our US entity," the group's global chief executive Alex Cornelissen said in a statement.

"Sea Shepherd Global and all other entities around the world, other than the USA, will continue to oppose the illegal Japanese whaling in the Antarctic," it added.

The whaling institute insisted the settlement would act as a deterrent to "some extent" by choking off funding by the group's US arm.

The announcement comes after a US court issued a preliminary injunction against Sea Shepherd in late 2012, ordering it to steer clear of the whaling ships.

Last year, the group agreed to pay $2.55 million to Japanese whalers for breaching the earlier court order.

Japan initiated the legal battle after several hunts in which the anti-whaling activists pursued the fleet for months in the icy waters near Antarctica, seeking to stop the slaughter.

Activists harassed whalers with paint and stink bombs, rammed their ships, and snared ship propellers with ropes.

Japan claims it conducts vital scientific research using a loophole in an international whaling ban, but makes no secret that the mammals ultimately end up on dinner plates.

It was forced to call off the 2014-2015 hunt after the United Nations' top court, the International Court of Justice, ruled in 2014 that its annual mission to the Antarctic was a commercial hunt masquerading as science.

The hunt resumed at the end of 2015, with the fleet returning to Japan in March of this year after having killed more than 300 of the mammals.