It said the shooter was also killed in the incident, but gave no further details.
The announcement came as a suicide car bomber in the capital Kabul struck a US-run NATO bus travelling through the southwest of the city, killing at least 17 people, including 13 US soldiers.
General Abdul Hameed, commander of 205 Atal corps in the south, said an Afghan soldier with three years' experience had carried out the shooting.
"At around 8.30 this morning (3pm AEDT), an ANA soldier named Darwish who had been serving as an ANA soldier for the past three years opened fire on a group of Australian military officers, killing three of them," said Hameed.
"The attacker was also gunned down by ISAF soldiers."
It's not the first time an ANA soldier has killed an Australian soldier.
In May this year, 25-year-old Lance Corporal Andrew Gordon Jones was shot dead by a rogue ANA soldier at the Patrol Base Marshal in the Chora Valley.
Fears of infiltration within the Afghan army ranks have risen as Western backers fund and train a huge expansion of the fledgling national force ahead of the withdrawal of all foreign combat forces scheduled for 2014.
The death of the three diggers on Saturday is the single worst incident involving Australians since June last year when three members of the Sydney-based 2nd Commando Regiment died in a helicopter crash in Kandahar province.
A total of 32 Australian soldiers have now been killed in a decade of involvement in Afghanistan.