Scott Morrison will become the first foreign leader to meet the new Japanese prime minister when he flies to Tokyo next week.
The prime minister stressed the importance of meeting Yoshihide Suga face-to-face.
"For many, many months now I have engaged in telephone diplomacy on a large number of matters," he told reporters in Canberra on Thursday.
"To be the first national leader to engage in Japan with the new prime minister, and to have the opportunity to do that, is significant for Australia."
Mr Morrison said the "very special relationship" with Japan was not simply based on economic, trade or cultural ties.
"Importantly, it a strategic one that we form together with the United States and India, a very important quad relationship," he said.
"Japan and Australia are very important together in providing, I think, a like-minded alignment on these strategic issues within our region.
"So the opportunity to go there and conclude some very important arrangements in this space is in Australia's national interest. While I am there I have the opportunity to discuss economic issues as well."
The leaders are likely to discuss Chinese expansionism, the coronavirus pandemic and a proposed travel bubble between their two nations.
The prime minister will visit Papua New Guinea on his way back to Australia, meeting Prime Minister James Marape.
"While I have spoken to Pacific leaders regularly throughout this crisis, this is an important opportunity to do that face-to-face," he said.
"We will actually happen to be in Port Moresby the night of the next State of Origin, so I suspect we will take a moment to watch that game together, as we like to do."
The prime minister and his delegation will go into isolation for 14 days when they return to Australia.
He plans to join Question Time in federal parliament via video link from The Lodge.
"It will be a first and I can only look forward to that, as I am sure all of you will also," Mr Morrison said.
The prime minister said recent overseas trips by the defence and foreign ministers showed international travel could be done safely.
Ahead of his overseas trip, he will take part in annual ASEAN and East Asia Summits via video link this weekend.