Australia's threat to take Japan to the International Court of Justice if it does not stop whale hunting is "unfortunate", FM Katsuya Okada says.
Mr Okada said Japan would defend its "legal" activities, but his Australian counterpart said Canberra wanted a halt "within a reasonable period of time".
Both men, however, insisted the issue would not harm strong bilateral ties.
On Friday, Australian Prime Minister Kevin Rudd gave Japan until November to stop whale hunting in the Antarctic.
His Foreign Minister, Stephen Smith, said his country could present its position before the International Whaling Commission (IWC) as early as Monday.
The Japanese fleet kills hundreds of the animals during annual hunts in Antarctic waters.
Its ships have been involved in repeated clashes with campaigners in recent weeks.
Japan abandoned commercial whaling in 1986 after agreeing to a global moratorium.
But international rules allow it to continue hunting under the auspices of a research programme.
Conservationists say the whaling is a cover for the sale and consumption of whale meat.
Current Japanese programmes aim for a total catch of more than 1,000 whales per year.
Japan's foreign minister made the comments after two days of talks in Australia.
"It's very unfortunate the Australian side has indicated it will take action in an international court," Mr Okada said in the city of Perth after meeting Mr Smith.
"Should action become a reality Japan will seek to represent its case with the IWC that its activities are legal," he said.
Mr Okada met Prime Minister Rudd on Saturday.
Mr Rudd has said his country will seek ICJ arbitration if it fails to resolve the issue with Japan.
Australia enjoys support from its traditional allies - New Zealand, the EU and the US.
Iceland and Norway also practise whale hunting.
In January, anti-whaling activists accused a Japanese vessel of ramming their high-tech speed boat during a confrontation in the Southern Ocean.
Video of the incident appeared to show the Japanese ship severely damaging the Ady Gil, but all six crew were rescued.