19/12/2015 8:29 AM AEDT | Updated 15/07/2016 12:51 PM AEST

Malcolm Turnbull and Shinzo Abe In Bilateral Talks

EUGENE HOSHIKO via Getty Images
Australian Prime Minister Malcolm Turnbull (L) and Japanese Prime Minister Shinzo Abe (R) attend a tea ceremony hosted by Sen Soshitsu (not in picture), the Grand Tea Master at the Tokyo headquarters of the Urasenke school of tea ceremony in Tokyo on December 18, 2015. AFP PHOTO / POOL / Eugene Hoshiko / AFP / POOL / EUGENE HOSHIKO (Photo credit should read EUGENE HOSHIKO/AFP/Getty Images)

Malcolm Turnbull has wrapped up his first visit to Japan as Prime Minister, expressing concern about the country's whaling program in bilateral talks with Japanese Prime Minister Shinzo Abe.

The two leaders have also discussed regional security and economic ties.

On the whirlwind trip to Japan Mr Turnbull told Abe of Australia's "deep disappointment" about Japan restarting its whaling program.

Turnbull said it was a matter of "real concern" to Australians.

"Nonetheless, we are very good friends and what good friends do is when they have differences they lay them out openly and honestly and in that way perhaps over time will be able to resolve them," he said.

Japan says that its plan to hunt 333 minke whales in 2016 as part of a scientific program.

Japan insists that violence from anti-whaling activists is unacceptable.

Turnbull also addressed the contested Senkaku islands in the South China Sea.

"Actions which disrupt, which create tensions, which raise the risk of conflict, whatever the motives of those responsible, will result in loss for everybody," Turnbull said.

"We all have a vested interest in the maintenance of a peaceful international order."