A former Afghan national army soldier who allegedly killed three Australian soldiers last year has been captured, the Defence Force has announced.

Former Afghan sergeant Hekmatullah is alleged to have shot dead Lance Corporal Stjepan Milosevic, Sapper James Martin and Private Robert Poate in the green-on-blue attack in Uruzgan province last August.

Two other soldiers were injured in the attack, before the assailant fled the scene.

The Chief of the Defence Force, David Hurley, says Hekmatullah is being held by Afghan authorities and will be charged with murder.

"Former sergeant Hekmatullah was apprehended by the inter-services intelligence, or ISI, in Pakistan and subsequently deported to Afghanistan through the efforts of the Afghan national directive of security and ministry of foreign affairs," he told a media conference.

"We expect to him face trial for the murder of Lance Corporal Stjepan Milosevic, Sapper James Martin and Private Robert Poate during an insider attack in Afghanistan."

General Hurley says he was advised of the apprehension in February but it could not be announced until Hekmatullah's transfer to Afghan authorities was completed.

The three fallen soldiers were all from the 3RAR Task Group based at Brisbane's Gallipoli Barracks.

Sorry, this video has expired Chief David Hurley says Afghan sergeant Hekmatullah in custody

General Hurley says their families have been informed of Hekmatullah's capture.

"This was bittersweet news for the families," he said.

"On the one hand, there is a great sense of relief, but it will not change history.

"This news comes at a difficult time for the family so close to the anniversary of the event.

"I extend my deepest sympathy to them and we will continue to support them as they come to terms with this latest development."

Father relieved that Hekmatullah was caught

Private Poate's father, Hugh, says he is relieved to hear Hekmatullah has been captured.

Mr Poate says it is the best news he has received in more than a year.

"A great sense of relief actually. It's another step forward in the recovery process for having lost our son," he said.

"It had been a long time - we always hoped that they would catch him."

Acting Opposition Leader Chris Bowen has congratulated those who helped capture Hekmatullah.

"I think that is a very positive development and of course today our thoughts go to the families that are dealing with this news and processing the news," he said.

"It would obviously be a difficult day for them, as well as a positive day for the nation."

Hours after the attack, two other Australians were killed in a helicopter accident in the Helmand Province, making it the deadliest 24 hours for Australia's combat troops since the Vietnam War.