Australia and Japan still don't see eye-to-eye over whaling but they're determined not to let the problematic issue disrupt an otherwise strong relationship.

Foreign Minister Stephen Smith canvassed the ongoing disagreement over Japan's so-called scientific whaling program with his Japanese counterpart Hirofumi Nakasone on the sidelines of the APEC foreign ministers' meeting in Lima on Wednesday (Thursday AEDT).

As the Japanese whaling fleet set sail on its annual Antarctic hunt earlier this week, Australia unveiled a $4 million program aimed at convincing its ally that the mammals don't need to be killed to be studied.

Japan has a target of about 935 minke and 50 fin whales this season.

Australia is strongly opposed to the whaling program but has so far failed to act on threats to consider international legal action against Japan.

Mr Smith said Australia and Japan were using "all diplomatic means" to resolve the issue, including discussions between Canberra's special envoy Sandy Hollway and officials in Tokyo.

"We continue to press the point," he told reporters.

"It's a difficult issue between the two nations but Foreign Minister Nakasone and I agree ... that it is very important for two things to occur: that the disagreement over whaling not become an issue that was out of proportion to the fundamental strength of the relationship and ... that we do our best to resolve it diplomatically."

"We ... agreed that we should seek to resolve the whaling issue by diplomatic means, both bilateral diplomatic means and multilateral diplomatic means ... through the IWC [International Whaling Commission]."

During the discussions, Japan pressed its point over the actions of international anti-whaling activists, which it regards as illegal.

"Foreign Minister Smith stressed that the Australian Government is making a clear distinction from the illegal action taken by anti-whaling groups," a Japanese Foreign Ministry official said.

However, according to the Japanese official, Australia was coy when asked about whether it would act to crack down on the groups.

"There was no particular reply from the Australian side," they said.

AAP, AFP