Five Australian troops were killed in two separate incidents in Afghanistan in what Prime Minister Julia Gillard on Thursday described as the nation's deadliest day in combat since the Vietnam War.

The deaths, which included three killings in an "insider attack" by an Afghan solider, brought to 38 the number of Australian lives lost in the conflict.

"This is a very big toll... this is our single worst day in Afghanistan," said Gillard, who cut short a trip to the Pacific Islands Forum to return home and deal with the fallout.

"Indeed this is the most lost in combat since the days of the Vietnam War."

Australia's acting defence chief Air Marshal Mark Binskin said the first incident occurred inside a patrol base near Tirin Kot in the restive southern Uruzgan province where about 1,500 Australian troops are deployed.

In the second, two Australian special forces soldiers were killed when their helicopter crashed in Helmand province.

Taliban insurgents claimed to have shot the aircraft down.

"Last night in Baghran district of Helmand province mujahideen (holy warriors) shot down a big logistics helicopter during fighting. Several foreigners were killed," Taliban spokesman Qari Yousuf Ahmadi said on his Twitter account.

The Taliban regularly exaggerate their battlefield operations.

"Three Australian soldiers from the 3RAR task group were shot and killed when an individual wearing an Afghan National Army uniform opened fire with an automatic weapon from close range," Binskin told reporters.

The dead soldiers were aged 40, 23, and 21 and were relaxing at the end of the day when the Afghan opened fire, he added.

Afghan President Hamid Karzai expressed his condolences over the incident.

"The attacks by Afghan security forces on foreign forces that have been happening recently, are the work of those who want to create distrust between Afghan national forces and their international allies," he said.

NATO Secretary General Anders Fogh Rasmussen also offered his condolences.

The alliance has struggled to counter the so-called "green-on-blue" attacks in which uniformed Afghans turn their weapons against their international allies.

The assaults have spiked this year, with more than 30 attacks claiming the lives of 45 coalition troops, comprising about 14 percent of the overall death toll in the war for 2012, according to ISAF.

The latest deaths are the third "green-on-blue" incident involving Australian soldiers.

Gillard admitted the spate of "insider attacks" was making it difficult to build trust between Australians and the Afghans they are training.

"It is really difficult for our soldiers in the field," she said, but insisted she still had faith in the progress Australian troops were making in Afghanistan.

"Our strategy is well-defined, our strategy is constant, and we cannot allow even the most grievous of losses to change our strategy," she told reporters in the Cook Islands.

"We went there for a purpose and we will see that purpose through."

Australia is a close ally of the United States and its Afghan deployment began in 2001. Canberra later pulled out, only to redeploy in 2005.

Australia announced this year that it would begin withdrawing its forces in 2013, earlier than planned due to significant security gains and as Canberra has faced increased pressure over the long-running Afghan campaign.