Former Afghan National Army sergeant Hekmatullah was captured by Pakistan's Inter-Services Intelligence in February and recently deported to Afghanistan, Defense Force Chief Lt. Gen. David Hurley said.
"Overnight, he was deported to Afghanistan where he is expected to face trial" charged with three murders, Hurley said in a statement.
"We have been relentless and determined in our efforts to pursue those who have murdered and wounded our people," he added.
Hekmatullah allegedly fired 10 to 15 shots within a patrol base north of the Australian military headquarters at Tarin Kowt on Aug. 29. He is accused of killing three Australian soldiers and wounding another two as they were playing cards, then fleeing.
An Australian Defense Department inquiry said last week that security before the attack was too weak given the Afghan army's open access to the administration area where the shooting occurred and the Australian soldiers' relaxed disposition. Many Australians were not wearing body armor.
Three Australian soldiers are expected to be disciplined over the security gaps. No motive for the shooting has been revealed.
Attacks carried out by uniformed Afghans were alarmingly common in 2012 but have happened far less often since a series of preventive measures were adopted by U.S. and coalition troops late last summer.
The killings eroded confidence between the sides at a crucial turning point in the conflict. So-called insider attacks killed 62 personnel in 47 incidents last year, according to NATO.
Australia was notified of Hekmatullah's capture in February. The Pakistani government had been working since then to arrange a proper transfer of Hekmatullah to Afghanistan, Hurley said.
Two Australian spy agencies— Australian Secret Intelligence Service and the Defense Intelligence Organization—had worked with Pakistan's ISI and the Afghan National Directorate of Security for six months to facilitate Hekmatullah's detention and deportation, he said.
Hakmatullah's arrest means that the suspects in all four so-called green-on-blue attacks on Australian soldiers have been captured or killed.
These insider attacks have killed seven Australians and left another 10 wounded.
Australia has 1,550 troops in Afghanistan and makes the largest military contribution of any country outside NATO. Australia has suffered 40 fatalities during more than a decade of fighting in Afghanistan.