A US court has declared the conservation group Sea Shepherd to be "pirates" and ordered it to stop its aggressive actions against Japanese whalers.

The ruling was issued on Wednesday by chief judge Alex Kozinski of the 9th US circuit court of appeals.

In his 18-page opinion, he wrote: "You don't need a peg leg or an eye patch. When you ram ships; hurl containers of acid; drag metal-reinforced ropes in the water to damage propellers and rudders; launch smoke bombs and flares with hooks; and point high-powered lasers at other ships, you are, without a doubt, a pirate, no matter how high-minded you believe your purpose to be."

The lawsuit was brought by a group of Japanese researchers who hunt whales in the Southern Ocean, collectively referred to in the judgment as "Cetacean". Their legal action to halt Sea Shepherd comes after years of clashes at sea.

The appeals court also sharply criticized judge Richard Jones who presided over the original case. His decision raises "doubts as to whether he will be perceived as impartial in presiding over this high-profile case", Kozinski wrote.

As a result of Wednesday's ruling, which grants Cetacean an injunction against Sea Shepherd, the American branch of the conservation group has severed ties with its Australian counterpart. Cetacean currently faces legal action from Australia, which has banned all whaling in its waters, a fact which Judge Kozinski noted, but reasoned: "It is for Australia, not Sea Shepherd, to police Australia's court orders."

Scott West, a spokesman for Sea Shepherd, told the Guardian that Kozinski's opinion is "only an opinion", and that the label of "pirate" is "ludicrous" given that "there is no personal gain, and there's no violence". The case will be transferred to a district court, though Sea Shepherd may choose to appeal against the injunction.

Yoshimasa Hayashi, Japan's fisheries minister, has reaffirmed the country's stance on whaling to the AFP, stating: "So why don't we at least agree to disagree? We have this culture, and you don't have that culture."

Although an international treaty has banned commercial whaling for 25 years, certain countries have permits to legally hunt whales for scientific research, including Japan and Norway. Sea Shepherd contends that "no reputable scientist will say this is scientific research", but international laws on open waters remain divisive and murky in practice.

This case comes in the shadow of a larger debate on whaling, dolphins and commercial fishing, as the WTO ruled that the US must end its "dolphin-safe" label program or grant exemptions by 2014, a decision that has sparked a row between conservation groups.

Dolphins, which are whales and also subject to similar hunts, have been protected by US policies since the 1999 Agreement on the International Dolphin Conservation Program. The program stipulates that fishermen cannot chase dolphins in order to round up the tuna swimming beneath them; in the process of netting fish, the boats raise dolphins, as well, which consequently suffocate. Mexico, which did not join the program, filed the suit with the WTO.

Organizations like Earth Island Institute, which monitors tuna companies to ensure safe practices, bemoaned the decision, citing several central American countries that will increase dolphin-chasing in newly unregulated environments.

Other groups, however, like the Campaign for Eco-Safe Tuna support the WTO ruling as a victory for a more sustainable fishing. They contend that the label program permits a lack of oversight, as well as a restrictive definition of safe practices, which inflicts greater harm on dolphins and other marine life via accidental catches, or "bycatch". The Campaign for Eco-Safe Tuna supports adopting a new label, which would remove the false pressure on fisherman to use the previous label over more sustainable methods of fishing