Malcolm Turnbull will express Australia's "deep disappointment" at Japan's resumption of whaling when he meets with Shinzo Abe in Tokyo.
Mr Abe is expected to reinforce Japan's interest in winning the tender for Australia's next generation of submarines during Mr Turnbull's first leader-level visit to North Asia.
The two leaders have already met in recent months at the G20, APEC and ASEAN summits, but Friday's Tokyo visit will be Mr Turnbull's first opportunity to discuss trade, investment, security and whaling at length with his Japanese counterpart.
Mr Turnbull wants to have what senior officials describe as an open and frank discussion and express Australia's "deep disappointment" at the resumption of whaling, which Japan says is scientific research.
Australia is exploring legal options with other like-minded nations to stop Japan approving lethal whaling in the Southern Ocean this summer.
The government argues Japan should respect the International Whaling Commission's procedures and advice and accept that there is no scientific basis to include lethal methods in the whaling program.
Greenpeace campaigner Nathaniel Pelle said Mr Turnbull should turn diplomatic rhetoric into a global action plan to stop what was clearly "commercial whaling".
Mr Turnbull will also use the trip to promote his innovation agenda, meeting with Japan's first astronaut Mamoru Mohri, who is director of the national innovation museum, Miraikan.
A number of new agreements are expected to be signed following a roundtable with Japan's leading researchers.
Mr Turnbull will deliver a lunchtime business speech and launch a new promotion for Australian food and wine.
Japan is competing with Germany and France for the contract to replace Australia's Collins class submarines.
Formal bids from the three countries are being assessed by the government.