An Afghan soldier accused of shooting dead three Australian troops in an insider attack was captured in Pakistan and is expected to be tried for murder, officials said Wednesday.

General David Hurley, chief of the Australian Defence Force, said the Afghan National Army Sergeant, Hekmatullah, was arrested by Pakistan intelligence officials over the August 2012 shooting at a small patrol base in southern Uruzgan province.

"Overnight, he was deported to Afghanistan where he is expected to face trial for the murder of Lance Corporal Stjepan 'Rick' Milosevic, Sapper James Martin and Private Robert Poate during an insider attack at Patrol Base Wahab in Afghanistan," he said.

Australia was first notified of Hekmatullah's capture in February and negotiations had been under way since then to arrange his transfer from Pakistan.

The defence ministry in Afghanistan and the foreign ministry in Pakistan, which handles deportations, declined to comment.

Hurley said Australian intelligence officials had worked closely with agencies in Pakistan and Afghanistan on the detention and deportation.

"We have been relentless and determined in our efforts to pursue those who have murdered and wounded our people," he said.

"We will continue to cooperate with Afghan authorities as they prosecute the case for justice for these Australians."

An internal military report into the insider attack released last week was highly critical of security measures in place at the time Hekmatullah allegedly opened fire on his colleagues with an automatic weapon.

The men had been playing cards or a board game and relaxing at the base some 20 kilometres (12 miles) from the main post at Tirin Kot, with force protection arrangements at the minimum authorised level.

The Australians were not in a state of readiness, with some soldiers wearing gym gear. Hekmatullah appeared to have acted independently of Taliban insurgents and there had been no warning signs.

Hurley said the dead soldiers' families had been informed of Hekmatullah's capture, news of which came at "a particularly difficult time for the families so close to the anniversary of the incident".

"Hekmatullah's capture draws a line under the four insider attacks on Australian personnel," he added.

"Those responsible for the deaths of seven Australian soldiers and who wounded another 10 have been captured or killed and no longer pose a threat to ADF personnel."

Attacks in which Afghan forces turn their guns on their international partners have killed scores of foreign soldiers, breeding mistrust and undermining efforts to train up local forces before NATO combat troops withdraw next year