Australian Prime Minister Malcolm Turnbull on Friday told Japanese Prime Minister Shinzo Abe of his "deep disappointment" over Tokyo's resumption of whaling in the Antarctic Ocean, though held out hope for a resolution of the highly charged issue.

Turnbull and Abe held talks on the occasion of the Australian leader's first visit to Japan since becoming prime minister in September.

"I have expressed today to the prime minister as I have before our very deep disappointment with Japan's resumption of whaling," Turnbull told reporters at a joint appearance with Abe after their talks.

Turnbull called it a "principal concern" for Australia and other countries, but added that Tokyo and Canberra are "good friends" that can openly express their differences.

"That way, perhaps over time, we will be able to resolve it," he said. "Let us hope so."

Despite tensions over whaling, the two countries have a flourishing relationship in trade and tourism and have moved to strengthen defence and security ties.

Japan is hoping to supply Australia's next generation of submarines but is in competition with French and German bidders in a deal worth up to Aus$50 billion ($35.7 billion).

A Japanese whaling fleet set sail this month for the Antarctic after a one-year pause, sparking a formal protest from 33 countries led by Australia and New Zealand.

Tokyo said last month it planned to kill 333 minke whales for "scientific research" this season in spite of a worldwide moratorium and widespread opposition.

It also makes no secret of the fact that the animals' meat ends up on the dinner table or served up in school lunches, though consumption is miniscule.

The fleet's departure marked the end of a year-long hunting suspension prompted by a United Nations' International Court of Justice ruling in 2014 that the annual hunt was a commercial venture masquerading as research.

Australia took Japan before the court in 2010 to try to end the annual hunts.

- 'Extreme acts' -

Abe said that he explained Japan's views and way of thinking on whaling and asked for help in ensuring the safety of the mission.

"Regarding the fact that there are groups that conduct extreme acts to interfere (with whaling), I asked for necessary actions to be taken as we must not justify any act of violence," Abe said.

He did not name any specific organisations, but Sea Shepherd, an environmental group that has repeatedly clashed with Japanese whalers at sea, has vowed to follow the latest mission.

Turnbull, in comments earlier in the day, was careful to emphasise that differences over whaling would not damage overall ties.

He said that while Japan must understand the position of anti-whaling nations, it was "important" for them to "understand the Japanese position" as well.

Australia and Japan have also expressed concern about rising tensions due to overlapping territorial claims by China and several Southeast Asian countries in the South China Sea -- a vital global trade artery.

The two leaders on Friday called for the end to large-scale landfill and construction work for military purposes, according to a joint statement reported by Japan's Jiji Press.

The agency took the comment to refer to China's creation of artificial islands in the South China Sea.

Japan and Australia signed an agreement last year allowing for the transfer of Japanese defence equipment and technology to Australia and also reached a bilateral free trade agreement.

They are also among 12 nations that this year forged the Trans-Pacific Partnership free trade pact.