Accusing his government of failing to adequately fund defence, John Healey quit from the UK ministry in protest, resulting in the last-minute cancellation of a press conference planned with federal Defence Minister Richard Marles at a naval base in Portsmouth.
Cabinet minister Tim Ayres said Mr Healey's departure will have no effect on the AUKUS agreement.
"This is a partnership that has deep support across all three countries, political systems within the public service, and the defence agencies in all three countries," he told ABC Radio on Friday.
"There will be over the life of this agreement ... Â many ministers for defence for all three countries, many secretaries for war in the United States' case, who are there charged with delivering this program."
Under the $368 billion deal, Australia will buy three used Virginia-class submarines from the US, before new SSN-AUKUS boats enter service from the 2040s.
But both the US and UK are experiencing submarine production issues, with a British House of Commons defence committee finding "shortfalls or delays in funding" could threaten the delivery of the fleet.
Australia is relying on the pact to replace its ageing Collins-class submarines, which are now undergoing life-of-type extensions, which will keep them in the water a decade longer than their planned retirement date.
Greens defence spokesman David Shoebridge said the UK defence budget was in "complete meltdown".
"For the UK, AUKUS is a second or third-rate priority, and that's very clear," he told reporters.
"The Greens are the only political party in the federal parliament who says no to AUKUS, who says we should not be spending $400 billion chasing nuclear submarines that will never turn up."
Former naval officer Jennifer Parker said much like Australia, the UK was trying to make up for years of underfunding defence.
"We know for phase three of AUKUS, Australia will work with the UK for the design and they will have built the first one (SSN-AUKUS submarine) - none of this is at risk," she told AAP.
"The resignation highlights the UK is not spending enough on defence and this does need to be addressed."
Releasing his resignation letter to UK Prime Minister Keir Starmer, Mr Healey said the embattled leader has been unable to "commit the resources that the nation needs to defend the country at this time of rising threats".
