The Diggers are said to be in a serious but stable condition, after the rogue soldier opened fire with an automatic weapon and a grenade launcher.
Two Afghan soldiers were also hit in the attack at Charmistan in the Uruzgan province, and are reported to be in satisfactory condition.
The Australian soldiers are recovering in a Kandahar hospital and their families have been notified.
Defence Force chief David Hurley says it is too early to tell whether the latest shooting is linked to an earlier incident.
The latest shooting happened less than a fortnight after a rogue Afghan soldier opened fire during a parade in Kandahar province, killing three Australian soldiers and wounding seven others.
“We need to do some digging, further digging,” General Hurley said in Canberra, when asked whether defence knew of the motives for the shootings.
“If we can find out what triggered this, it’s going to be helpful to us.”
He says it’s a highly-complex issue and there are many factors at play that will require more examination and analysis.
Australian troops disarmed about 30 other ANA soldiers who were at the forward base following the shooting.
The gunman fled the scene of the shooting in one of the Afghan National Army vehicle and remains at large.
Generak Hurley said the soldiers were members of Mentoring Taskforce Three operating at a patrol base.
The ANA soldier “located in an over watch position” opened fire on both Australian and ANA soldiers.
“The three Australian soldiers suffered serious wounds and they received immediate first aid,” General Hurley said.
They were transferred by helicopter to a medical facility at Tarin Kowt before being transferred to Khandahar.