Australia has again expressed disappointment at Japan's failure to swap harpoons for science, as it embarks on its annual whaling hunt.

Four Japanese ships left port on Thursday for the Southern Ocean, where it plans to kill an unspecified number of fin whales, humpbacks and minkes for so-called scientific research.

There is a world-wide moratorium on commercial whaling, but Japan hunts whales under the banner of research.

Australia was deeply disappointed to see the Japanese government condone yet another annual slaughter, Environment Minister Peter Garrett said.

"The Australian government has said repeatedly that we do not have to kill whales to study them," he said in a statement.

"Japan has the opportunity to swap harpoons for science this summer."

Mr Garrett said the government was making an unprecedented effort to persuade Japan to stop the killing of whales, including the appointment of a special envoy.

The government has committed $32 million to non-lethal whale research.

But with the Japanese ships already headed south, opposition environment spokesman Greg Hunt said the government had failed to back up its election promise to hold the Japanese to account.

"This is the third summer of whaling since (Prime Minister) Kevin Rudd and Peter Garrett led Australians to believe they would stop the practice," he said.

"Their promised international court action goes down as one of the biggest broken promises of this government."

But Mr Garrett said the government had delivered on the promise, which was to collect evidence for possible legal action.

"That option remains on the table," he said.

The government was also working through other reforms, including giving greater powers to the International Whaling Commission "to make it a conservation-focused organisation, not one that simply counts dead whales".

"We will continue to pull out all stops in our diplomatic and other efforts," Mr Garrett said.

Japan issued its own permits for the slaughter of 950 whales in the 2008/2009 season.

It has not yet applied for permits this year.