The ministers also said they were committed to strengthening maritime law in the region.
Both nations have had to deal with protest actions at sea, including protests around oil exploration vessels off the coast of New Zealand and anti-whaling protests around Japanese vessels in the Southern Ocean.
The ministers said it was important to resolve disputes and issues peacefully, without force or provocation, in a way that was consistent with international law.
More generally, the statement said both nations were committed to bringing "new vigour and vision to the relationship".
The ministers stressed the importance of regional cooperation and trade talks, including the Trans-Pacific Partnership negotiations which both nations are party to.
They also expressed their shared concern over North Korea's nuclear weapons and missile development plans.
They urged the communist state to abandon all nuclear weapons activities and to address humanitarian and human rights concerns, including abductions.