Australian and Japanese forces will be able to seamlessly train in both countries, on each other's platforms and during humanitarian missions under a new reciprocal agreement.
Prime Minister Scott Morrison will sign the "historic" treaty during a virtual summit with his Japanese counterpart Fumio Kishida on Thursday.
"We could be completely interoperable between what we can do and how we deploy together," he told reporters ahead of the signing ceremony.
"I do not just mean hostile circumstances, I mean also in the Indo-Pacific for humanitarian purposes, (in) which Japan is very active, as is Australia."
Mr Morrison said the security treaty, being Japan's only reciprocal agreement, underscored its significance and highlighted the trust between the two countries.
He recalled standing with former Japanese prime minister Shinzo Abe at a war memorial in Darwin, saying it was one of the most important moments of his prime ministership.
"(It) is probably one of the most significant moments I can recall ... to stand with the Japanese prime minister honouring our fallen in Australia from the second World War.
"I cannot put into words what it is about, and here we are, two countries, a few generations later, concluding an agreement such as this, it is truly breathtaking and remarkable."
The agreement has been in train for more than half a decade, emerging under former prime minister Tony Abbott.
Mr Morrison said he had worked with three Japanese prime ministers over as many years to ink the landmark treaty.
"It has been a long journey ... and I am pleased with being able to get to this conclusion," he said.
Japan's Ambassador to Australia Shingo Yamagami welcomed the agreement, telling AAP it was a new chapter in the two countries' security co-operation.
"In light of the deteriorating security environment, what Japan and Australia can do together is first of all to increase deterrence," he said.
Japan is Australia's only special strategic partner which in diplomacy is just below an ally, with Mr Morrison labelling the country as "one of our most important partners".
The treaty follows China's criticism of the Quad partnership formed between Australia, Japan, India and the US, as well as the AUKUS pact, under which Australia is exploring the purchase of nuclear-powered submarines.
When asked about the treaty at a daily news briefing in Beijing on Wednesday, Chinese Foreign Ministry spokesman Wang Wenbin said bilateral treaties should promote regional trust, peace and stability.
"It should not target or harm any third party interests," Reuters quoted him as saying.
The treaty will also enable Japan and Australia to collaborate on clean energy and critical technologies.
"Our co-operation also includes an expanding agenda for the Quad with India and the United States, and our shared technology-led approach to reducing carbon emissions," Mr Morrison said.
Australia Japan Business Co-operation Committee president Peter Grey told AAP the treaty was another example of the broadening relationship between the two countries.
"Mutual trust built on decades of successful commercial activity in key areas for both countries ... has been a key facilitator of such developments, and we expect our business connections to continue to expand apace," he said.