The Federal Government has announced it will launch legal action against Japan's whaling program in the International Court of Justice next week, but Foreign Affairs Minister Stephen Smith says he does not think the move will hurt the relationship between the two countries.

Formal proceedings against Japan's Southern Ocean whale hunt will be lodged in The Hague ahead of an International Whaling Commission (IWC) meeting in Morocco in June.

Mr Smith informed Japan of the decision last night, after it was approved by Federal Cabinet yesterday afternoon.

He says he is confident the legal action will not affect Australia's bilateral relationship with its major trading partner.

"The agreement between Australia and Japan is that we will treat this matter in a calm, responsible and mature way," he said.

Federal Environment Protection Minister Peter Garrett joined Mr Smith for the announcement and said Japan's so-called scientific whaling program must end.

"We want to see an end to whales being killed in the name of science in the Southern Ocean," Mr Garrett said.

Mr Garrett was also confident the legal action would not affect Australia's bilateral relationship with Japan.

"It's a disagreement between friends, but it is a disagreement which we now believe needs to be properly resolved in the appropriate forum," he said.

"In the run-up to the IWC my expectation is that that will be an extremely intense and difficult negotiation, but it's clear to us that this was the appropriate time to lodge that action."

Prime Minister Kevin Rudd's pledge to take Japan to the international court was a key plank of Labor's federal election platform in 2007.

Hidenobu Sobashima from Japan's foreign ministry has told the ABC that Tokyo is disappointed by the decision.

Japan describes the legal action as ""regrettable" but says it is confident the legal action will not harm relations between the two close allies.

But it says it is prepared to argue its case inside the court.

'Having the guts'

Jeff Hansen from the anti-whaling group Sea Shepherd says the Government's decision is a step in the right direction.

"Sea Shepherd commends the Australian Government for finally having the guts to stand up to the Japanese whalers," he said.

"But make no mistake - if the Japanese whaling fleet make their way down to the Southern Ocean whaling sanctuary this summer, Sea Shepherd will be there to stop them."

Mr Hansen has offered to help the Government collate evidence for its case.

"We're always open to share any information or documentation we have," he said.

"We have our log books and details where the Japanese whaling fleet is operating in and you can see clearly the whales are being hunted.

"They're operating deep within the Southern Ocean whale sanctuary and deep within the Australian economic exclusion zone."

Greens leader Bob Brown is pleased the Government is taking Japan to court but says it is too late to stop the whale hunt this summer.

"It's welcome but it's not enough. And a legal challenge now in the international court by the Rudd Government they know is not going to see any finality before the election," Senator Brown said.

"It is very careful election engineering rather than any sort of stay of the harpoons."

Opposition Leader Tony Abbott would not say if he supports the move because he has not seen the Government's legal advice, but he has a theory on the Government's motive for announcing the step today.

"Plainly, it is a smokescreen against the Government's latest attempt to brainwash the Australian people with a dishonest advertising campaign," he said.

"The Coalition strongly opposes so-called scientific whaling. We support appropriate and effective action in international tribunals."