Lowy Institute senior fellow Richard McGregor said: “Mattis was a good friend of Australia, understood alliances and treated Australia as a good friend.
“The Australian government will be as concerned as everybody else that he is going.”
It follows the sacking of Secretary of State Rex Tillerson and resignation of Mr Trump’s second national security adviser, HR McMaster, in March.
General Mattis resigned after President Trump’s announcement on Thursday the US would withdraw about 2000 American troops serving in Syria, claiming victory amid the country’s long-running civil war.
In his resignation letter to the US President, he wrote: “Because you have the right to have a Secretary of Defence whose views are better aligned with yours on these and other subjects I believe it is right for me to step down from my position.”
On Friday several unverified media reports emerged from Washington that the Trump administration will withdraw about 7000 troops from Afghanistan in the coming months, slashing its personnel commitment in half.
About 300 Australian defence personnel are based in Afghanistan to train Afghan forces fighting the Taliban.
A government source said there would be no official comment before any possible official announcement from the US on its commitments in Afghanistan.
Save taxpayer money
Defence Minister Christopher Pyne said in a statement that Mr Mattis had been a close friend of Australia and “established deep trust and respect among allies and partners in the Indo-Pacific region”.
“Secretary Mattis’ service is an example of why our alliance continues to be strong. His commitment to deepening ties with Australia and with other US allies has never been more important.
“I look forward to working closely with Secretary Mattis’ successor to further strengthen the Australia-US alliance.”
President Trump campaigned on cutting American resources in wars in the Middle East to save taxpayer money and the lives of American soldiers.
The upheaval just days before Christmas came less than 48 hours after Prime Minister Scott Morrison visited Iraq to thank special forces soldiers and other Australian Defence Force personnel training the Iraqi Army to combat the Islamic State terrorist group.
The government said a planned visit by Mr Morrison to Afghanistan had to be cancelled because of security concerns.
Former US defence policy adviser Jason Israel said Republicans and Democrats in Washington were disappointed Mr Mattis had quit.
Peter Jennings, executive director of the Australian Strategic Policy Institute, and a former government defence strategist, told The New York Times: “I had a discussion with a senior government official this morning and he asked: ‘Who’s left in the US Cabinet who we regard as an adult?’ We both scratched our heads.”
Tens of thousands of Australian soldiers have served in the Middle East since 2001.