The prime minister met with his Japanese counterpart Shinzo Abe during a one-day visit to Tokyo on Friday, as Japan prepared to resume what it describes as a scientific whaling program.
"I have expressed today to the PM, as I have before, our very deep disappointment with Japan's resumption of whaling," he told reporters in Tokyo at joint press conference with Prime Minister Abe.
"It's a matter of major concern, real heartfelt concern to Australians and other countries as well, as the PM knows. Nonetheless, we are very good friends and what good friends do is when they havedifferences they lay them out openly and honestly and in that way perhaps over time will be able to resolve them."
Senior officials say Australia is not ruling out international court action over whaling, but is focusing efforts on a diplomatic solution.
Australian Prime Minister Malcolm Turnbull, accompanied by his counterpart Shinzo Abe Source: AAP
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PM talks up Australia in Japan
With tension continuing in the South China Sea, Mr Turnbull encouraged Japan to work more closely with China and Korea, saying any military action which added to tension and disturbed the harmony of North Asia would "damage all our economies".
Australian and Japanese military forces are expected to continue joint exercises with the US in 2016.
Mr Turnbull shares Mr Abe's interest in innovation as a key driver of economic growth, having released an "ideas boom" strategy earlier this month.
He took a selfie with the world's most advanced humanoid robot ASIMO during a visit to the National Museum of Emerging Science and Innovation in Tokyo.
Japan has agreed to recognise Australian university degree qualifications from 2016 and deals were signed on Friday to deepen university ties in the area of energy, health and medical research.
Australian Prime Minister Malcolm Turnbull, left, shakes hands with Japanese chefs during an event of "Taste of Australia" Source: AAP
A round-table with leading researchers in innovation and Australian university vice-chancellors was followed by the signing of a new deal with Japan on regenerative medicine.
Regenerative medicine includes treatments around stem cells and gene therapy intended to restore the function of damaged organs and tissues.
The market in Japan for regenerative medicines is projected to grow to more than $17 billion by 2030, according to the Japanese government.
The deal involves greater collaboration between Austrade and Japan's peak industry body, the Forum for Innovative Regenerative Medicine.
Also on the agenda for the Turnbull-Abe meeting was Japan's bid to build Australia's next generation of submarines.
Japan, Germany and France are competing for the multi-billion-dollar contract to replace the Collins class submarines.
