It is expected any military exercises would involve the RAAF and would take place in Darwin.
Prime Minister Turnbull and Prime Minister Shinzo Abe are working towards establishing a defence agreement that would not only include joint exercises but also information sharing and defence industry collaboration.
The move comes as China's activity in the region rises, as well as the nuclear threat posed by North Korea.
"In a period of strategic uncertainty, both countries recognise the need to deepen security ties," PM Turnbull said.
"Prime Minister Abe and I are committed to strong defence co-operation through joint exercises, information sharing and defence industry collaboration. We are working to formalise this in our reciprocal access agreement that will further enhance our defence interoperability. We are trusted partners across a broad range of security interests such as cyber, counter-terrorism and disarmament, and there is the potential to collaborate further.
"The international community, and particularly partners in Asia, must work together to maximise pressure on North Korea and effectively implement UN Security Council sanctions against the regime."
The meeting comes as Japan and Australia mark the third anniversary of the Japan-Australia Economic Partnership Agreement. Japan is currently Australia’s second largest export market and Australia's largest direct investor in Asia.