A rogue Afghan soldier was on the run Wednesday after shooting and wounding three Australian troops, days after a similar incident left three Australians dead, the defence department in Sydney said.

The men suffered serious wounds but all were in a stable condition after an Afghan National Army soldier opened fire on them at Charmistan in Uruzgan province on Tuesday afternoon, the department said.

Two Afghan soldiers were also wounded.

The incident comes less than a fortnight after an Afghan soldier killed three Australians and wounded seven others when he opened fire during a parade in Kandahar province.

"It is too early to speculate that the two incidents are linked," defence force chief David Hurley told reporters.

"I stress that there is no simple one-line explanation to this incident or the previous incident.

"We need to do some digging, further digging," he added when asked whether he knew of the motive.

The latest shooting happened just days after Australian Prime Minister Julia Gillard visited Afghanistan, making an unannounced stopover to meet troops in the restive southern province of Uruzgan.

Australia has 1,550 troops stationed in the country, with 32 so far killed in the conflict.

Australian troops were first deployed to Afghanistan in late 2001 before being pulled out in 2002. They were redeployed to the war in 2005 and have been training Afghan soldiers in Uruzgan.