Troops disarmed In the Uruzgan incident on Tuesday afternoon, Australian officials said an Afghan soldier fired on colleagues with an automatic weapon and a grenade launcher at a patrol base in the Charmestan region, north-east of Tarin Kot.
Three Australian soldiers on a mentoring mission were seriously wounded and two Afghan troops lightly injured.
The attacker fled in an army vehicle and is still to be caught. All members of the Afghan base were disarmed and confined to barracks.
There has been a string of "rogue soldier" attacks on Western troops in Afghanistan.
Two weeks ago an Afghan soldier shot and killed three Australian troops and an Afghan interpreter in Kandahar, southern Afghanistan.
Australia has lost 32 soldiers during operations in Afghanistan.
The Nato-backed International Security Assistance Force (Isaf) is gradually handing over responsibility for security to Afghans but about 140,000 foreign troops remain in the country.
The handover is expected to be completed by the end of 2014.
The United Nations says the first six months of 2011 were the deadliest for civilians across Afghanistan since the war began in 2001.