Under the agreement, Australia has been promised at least three Virginia-class submarines from the US in the early 2030s, with a new class of nuclear-powered boats to be built for delivery from the 2040s.
Concerns have been raised over the increasing pressure the US submarine industrial base has come under, in addition to the president-elect's position on the deal struck under the Biden administration.
The government is confident AUKUS will be supported by the Trump administration. (Lukas Coch/AAP PHOTOS)
Mr Marles said the challenges facing the US was not news, and that Australia had taken the unprecedented step to making a "significant contribution" to the American industrial base to improve production rates.
"We are confident that, in terms of the trajectory of production which needs to be achieved in order for this to all play out, that we are on that pathway as we speak," he told ABC's RN on Monday.
"Everything that we have seen is what is playing out.
"All the agreements that we've asked to be signed and steps to be taken are being taken. AUKUS is happening, and it is on course."
Mr Marles pointed to bipartisan support in the US for AUKUS and the legislation passed in the Congress to enable the sale of the submarines to Australia.
"We can draw confidence from this because AUKUS is in the strategic interests of the United States as it, of course, is in the strategic interests of Australia and the United Kingdom.
"That's why, fundamentally, people support it across the political spectrum, in all three countries, and why we feel very confident about its progress over the next four years."
Foreign Minister Penny Wong is in Washington and will attend Mr Trump's inauguration ceremony on January 20.
She will meet members of the Trump administration and Congress during her visit.
Australia's ambassador to the US Kevin Rudd has also been invited.
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