Mr Morrison met with Japanese counterpart Yoshihide Suga in Tokyo on Tuesday, becoming the first world leader to meet with the new prime minister on Japanese soil since he took over from Shinzo Abe.

Mr Morrison and Mr Suga signed the Reciprocal Access Agreement that streamlines each country's use of the other's military bases.

The agreement needs to be ratified by parliament.

If finalised, it would be the first pact by Japan to allow a foreign military presence on its soil after a similar 1960 accord with the United States.

"This is a significant evolution of this relationship, but there is no reason for that to cause any concern elsewhere in the region," Mr Morrison said.

"I think it adds to the stability of the region, which is a good thing."

The RAA has been under negotiation since 2014 with the major sticking point being concerns that an Australian serviceman or woman could face the death penalty if convicted of murder or other serious offences on Japanese territory.

Asked how this issue had been "ironed out", Mr Morrison didn't specify, but said Australia would "meet all of its obligations under its international agreements".

Mr Suga said Japan and Australia are "special strategic partners" that are both committed to fundamental values such as freedom, democracy, human rights and the rule of law, and are working together to achieve peace and stability in the region.

In a joint statement, the two leaders expressed "serious concerns about the situation" in the South and East China Seas and "strong opposition" to militarising disputed islands and other unilateral attempts to change the status quo, without identifying China.

Australian Associated Press