Mr Morrison and Japanese Prime Minister Fumio Kishida formally inked the “Reciprocal Access Agreement” at a virtual meeting on Thursday.

Mr Kishida joined via video link after announcing he was cancelling his planned trip to Australia and the US earlier this week due to the rapid spread of Omicron in Japan and across the world.

Giving his remarks from the cabinet room of Parliament House during the ceremony, Mr Morrison said Japan was Australia’s closest partner in Asia.

“This is a landmark treaty which opens a new chapter for advanced defence and security co-operation, in what is a complex and rapidly changing world, something you and I both understand very well,” he said.

“This treaty will form an important part of Australia’s and Japan’s response to the uncertainty that we now face.”

A joint statement released after the meeting said the two leaders expressed serious concerns about the situation in the South China Sea and their “strong objection” to China’s unlawful maritime claims and activities inconsistent with the UN Convention on the Law of the Sea.

They also spoke about the East China Sea – where China claims sovereign territory to an uninhabited rocky island chain which is controlled by Japan.

“They... expressed strong opposition to any destabilising or coercive unilateral actions that seek to alter the status quo and increase tensions in the area,” the statement said.

Both Prime Ministers also shared concerns about the reported human rights abuses against Uyghur and other Muslim minorities in China, the joint statement said.

Speaking at an earlier press conference on Thursday, Mr Morrison said the new agreement was the only one of its kind Japan held with another nation.

“And that says something about the level of trust and partnership, a partnership of equals, standing up for the security of the Indo-Pacific, and the values as democracies that we hold very dear,” he said.

He said it complemented other agreements such as the AUKUS submarine deal and $1bn military contract with South Korea.

“This meshes together, it weaves together, this suite of agreements to ensure that Australia works with our partners to ensure that our region can be prosperous, can be safe, and can be open and can be free.”

China’s foreign ministry spokesman Wang Wenbin has warned that the new treaty should not “target or harm any third parties”.

“The Pacific Ocean is big enough for the common development of countries in the region,” he said this week when asked about the new agreement.

“Along the same line, peace and stability in the Pacific depends on the joint efforts of countries in the region.”