Australia is launching legal action to stop Japanese whaling in Antarctic waters.

The federal government promised to do this before the last election, but had recently deferred action until November 2010 at the earliest.

But on Friday, Foreign Minister Stephen Smith said the government would lodge a formal application in the International Court of Justice in The Hague next week.

"Australia will initiate action in the International Court of Justice, seeking to prevent Japanese whaling in the Southern Ocean," Mr Smith told reporters in Sydney.

Mr Smith said he spoke to his counterpart in Japan before the announcement and both of them agreed the case would not disturb the country's international relationship.

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

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

Japan's Foreign Ministry said it was regrettable that Australia was bringing the issue before the court while negotiations continue within the International Whaling Commission on disputes over whale hunts.

"We will continue to explain that the scientific whaling that we are conducting is lawful in accordance with Article 8 of the international convention for the regulation of whaling," said ministry Deputy Press Secretary Hidenobu Sobashima. "If it goes to the court, we are prepared to explain that."

Mr Sobashima said the issue "shouldn't jeopardise the overall good relations between Japan and Australia".

Mr Smith echoed that sentiment, saying the two countries have agreed to treat the matter as "an independent legal arbitration of a disagreement between friends".

He was resolute both countries had agreed to quarantine the legal action from the international relationship with Japan - one of Australia's biggest trading partners.

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

"Both nations adhere to the jurisdiction of International Court of Justice and we will treat this matter effectively as an independent legal arbitration of a disagreement between friends."

Mr Smith rejected the suggestion that the government has done a backflip on its previous stance.

"The cabinet came to the conclusion that we should initiate legal action and we should announce it today," Mr Smith said.

"We have said consistently that if we came to the conclusion that our objectives could not be met by diplomatic means, whether bilateral or multilateral diplomatic efforts through the IWC (International Whaling Commission), then we always reserved the right to initiate legal proceedings and that's what we've announced today."

Australian Conservation Foundation executive director Don Henry welcomed the announcement and said it was "about time".

"It is a very good step and it's nice to see that there is strong support for really questioning this abominable whaling from other countries and including the EU," Mr Henry told AAP on Friday.

And International Fund for Animal Welfare (IFAW) Asia Pacific director Erica Martin said the unprecedented move showed the government was willing to put their words into action.

"Whaling has no place in the 21st century," Ms Martin said.

Meanwhile, New Zealand will decide in the next few weeks whether it will follow suit.

"New Zealand has been disappointed by the progress of diplomatic negotiations in the International Whaling Commission (IWC), and we have made it clear that the current proposal is not adequate," Foreign Minister Murray McCully said today.

"However, we believe that there is still room to make progress before the IWC's annual meeting in Agadir in June.

"The Government has always said that action in the ICJ remains an option for New Zealand if the diplomatic process fails."