A US nuclear-powered submarine has pulled into Darwin Harbour, with authorities keeping the high-value vessel under close wraps from the public eye.

On Thursday morning, the USS Minnesota, escorted by a couple of tug boats, was seen passing through Darwin Harbour towards East Arm.

It is understood the USS Minnesota cruised to northern Australia directly from Perth, where it was docked at HMAS Stirling last month.

Last week, the NT Government issued a ‘notice to mariners’, warning local boaties the waters surrounding East Arm Wharf would be closed due to a joint US navy and ADF operation which runs until April 3.

Defence Minister Richard Marles has hosted his US and Japanese counterparts in Darwin for trilateral discussions on increased military cooperation.

Japanese troops will begin regular deployments in northern Australia as part of military cooperation between the three countries, Mr Marles announced on Sunday.

"Today we are announcing that there will be regular deployments of Japan's amphibious Rapid Deployment Brigade to Australia," Mr Marles said at a televised press conference in Darwin.

Mr Lander said he held deep reservations about the US military presence in Australia, with the former deputy ambassador maintaining the Top End was being weaponised by Washington DC in favour of American interests.

“The US is not preparing to go to war against China, it is preparing Australia to go to war against China,” he told a conference in Perth last week.

“It is preparing a number of countries in our region to be its proxies in such a war, as it has done using Ukraine in [the] war against Russia.”

“The likes of Sydney and Melbourne are a very long way away from Darwin, so people can often be psychologically removed from the problem. There is no physical presence of US military for most people in Australia, so they can remain complacent in grasping the reality of what is happening in our country.”

Japanese troops could join US marines for regular rotations through the Top End as Tokyo, Washington and Canberra continue to deepen defence and strategic ties in the face of China's swelling military might.

Next year, Australia will participate for the first time in Orient Shield, the largest annual field training exercise between the U.S. Army and Japan Ground Self-Defense Force.

Australia and Japan also plan to involve the Japanese Amphibious Rapid Deployment Brigade, a marine unit of the Japan Self-Defense Forces, in annual training rotations of U.S. Marines in the northern Australian city of Darwin.

The ministers agreed on more engagement in training exercises involving the two air forces after F-35A Lighting II stealth fighters from both countries joined in combat training over Japan last year in Exercise Bushido Guardian

Deployments of Japanese F-35 fighter jets to northern Australia will be ramped up as part of a deepening of security ties between the two countries, while Anthony Albanese prepares to join Quad leaders for a summit in the US later this month.

Late last month, Tokyo lodged a diplomatic protest after a Chinese spy plane allegedly breached its airspace for the first time near the Danjo Islands in the East China Sea.

Shared concern by Australia and Japan over Chinese aggression prompted the signing of a landmark defence pact that came into force last year, making it easier for each country’s military to operate in the other nation.

At Thursday’s 2+2 talks, ministers are expected to expand the rotation of Japanese F-35 fighter jets for temporary basing in Australia, including joint exercises alongside US Marines in Darwin. Two Japanese jets were dispatched to Australia a year ago to test the viability of deployments.

In a strongly symbolic message, the talks will be held at Queenscliff, east of Geelong – home of the secretive Swan Island defence and spy training facility.