Australian Foreign Minister Bob Carr says it's crucial that differences with Japan over its controversial whaling program do not extend to other areas in the relationship between the two countries.

Speaking after a bilateral meeting with his Japanese counterpart Fumio Kishida in Brunei on Monday, Senator Carr said he had re-stated Australia's objections to what Tokyo insists is a scientific whaling program.

The comments come as Japan prepares to deliver its opening submission in a case brought by Australia at the International Court of Justice (ICJ) in The Hague on Tuesday that challenges the validity of annual whale hunt in the Southern Ocean.

But while again condemning the practice, Senator Carr also said that the depth of the relationship between Tokyo and Canberra went far beyond one issue, and that care must be taken to ensure that strong relationship continued.

"We are strongly opposed to whaling even when it's described as scientific whaling as it is by the Japanese," Senator Carr told AAP.

"But with the Japanese we quarantine our differences over this subject from the rest of our strong relationship because it's so important to both Japan and Australia.

"I'm confident we can handle the case in the court sensitively to minimise any negative public perceptions in Australian or Japanese circles."

Senator Carr said he believed that Japan would honour any decision made by the ICJ.

"I think they would have to abide by it."

Australia, which last week made its opening arguments in the case which has been brought after the failure of years of diplomatic efforts to resolve the matter, wants the 16-judge panel to rule that Japan's whaling program isn't science-based.

The Australian side argues that the annual hunt breaches the 1946 whaling convention which only allows harpooning "for purposes of scientific research".

But Tokyo points to the convention's preamble which states its aim is "the proper conservation of whale stocks".

Japan last week seized on comments from an expert witness for Australia that the program isn't a threat to minke stocks and therefore does conform to the convention.

During hearings at The Hague last Thursday, US mathematics professor Marc Mangel admitted Japan's target of catching 850 minke whales in the Southern Ocean each year "will not in any way endanger the stock".

Australian lawyer James Crawford had argued that the whaling program isn't based on real science, but in fact is "a parody of science".

The case was finally brought this year after years of diplomatic pressure from Canberra, and after Prime Minister Kevin Rudd who as opposition leader first pledged to take Tokyo to court while campaigning to become prime minister in 2007.