Prime Minister Scott Morrison choked back tears as he read the names Thursday of 41 Australians killed in Afghanistan to mark the end of his country's involvement in the 20-year war.

Speaking at a televised news conference, Morrison said Australia would remove its remaining troops from Afghanistan in September in line with the US decision to ends its military operations there.

Australia deployed 39,000 troops over the past 20 years as part of US and NATO-led operations against the Taliban and terrorist groups in Afghanistan, but has only 80 support personnel there today.

Morrison called the decision to leave Afghanistan "a significant milestone in Australia's military history" that marked the end of a costly chapter for the country's defence force.

He then read out the names of the 41 Australian soldiers killed in the conflict, halting several times as he choked back sobs, especially when mentioning Brett Till, a 31-year-old sergeant from his own Sydney constituency.

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"The loss is great. The sacrifice immense," he said.

"These brave Australians are amongst our greatest ever, who have served in the name of freedom."

While Australia has not had a significant troop presence in Afghanistan in recent years after withdrawing its combat troops in late 2013, the war continues to take a toll and fuel controversy at home.

Veterans groups have pressured the government into launching a formal inquiry into a high number of suicides among Afghan veterans and other ex-servicemen and women.

The military and police are both actively investigating numerous war crimes alleged to have been committed by members of elite Special Air Services soldiers in Afghanistan.

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