Accusing his government of failing to adequately fund defence, John Healey quit from the UK ministry in protest overnight, resulting in the last-minute cancellation of a press conference planned with Defence Minister Richard Marles at a naval base in Portsmouth.
The key media event was going to outline both nations' aspirations for the AUKUS partnership.
Cabinet Minister Tim Ayres said Mr Healey's departure will have "no effect" on the crucial security pact.
"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 the 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 new fleet.
Australia is relying on the AUKUS agreement to replace its ageing Collins-class submarines, which are now undergoing life-of-type extensions to keep them in the water a decade longer than their planned retirement date to prevent a capability gap.
Releasing his resignation letter to UK Prime Minister Keir Starmer, Mr Healey said there were credible ways of meeting funding challenges to protect his country's ability to deliver on the missions of their government.
"You have been unable, and the Treasury has been unwilling, to commit the resources that the nation needs to defend the country at this time of rising threats," he wrote to Mr Starmer, who has faced increasing calls from colleagues to step down as leader.
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