Two more Australian soldiers have died in Afghanistan in a "very bad day" for the Defence Force, Air Chief Marshal Angus Houston has announced.

One of the soldiers was a 25-year-old, Queensland-based lance corporal who was shot by an Afghan National Army soldier with whom he was serving on guard duty at a patrol base in the Chora Valley.

The Australian, from the Mentoring Task Force, was airlifted to the Australian base at Tarin Kowt but died from his wounds.

The Afghan soldier fled the scene and escaped despite being shot at by another Afghan soldier.

Afghan and Australian forces are now hunting for the gunman, described as a "rogue soldier" by Air Chief Marshal Houston.

The dead soldier had served in East Timor and started his tour in Afghanistan last November.

The other was a Victorian-based pilot, a 27-year-old lieutenant travelling as a passenger in a Chinook helicopter that crashed during a resupply mission 90 kilometres east of Tarin Kowt.

It is not known if the crash was the result of enemy action.

The dead officer had recently flown helicopter rescue missions for the ADF during the Queensland floods.

Five other Australians in the helicopter were not seriously hurt.

Air Chief Marshal Houston said the first soldier was on sentry duty in the guardhouse with two Afghan soldiers when the shooting occurred.

"One of the Afghan soldiers departed to attend to a personal matter, and it was during his departure that the incident occurred," he said.

"Shots rang out and the Afghan who was attending to a personal matter came back and found our member badly wounded and applied first aid and raised the alarm.

"He also fired at the absconding Afghan National Army member."

Air Chief Marshal Houston said the Australian soldier sustained three wounds "which might suggest three shots, but until we do the investigation I would not confirm that".

Vetted

He said all Afghan soldiers enrolled in the ANA are vetted by NATO recruiters.

"We work very closely with them. We observe them and we are always on the lookout for anybody who behaves in a strange way.

"They are the sort of protections we have in place, and obviously we will have another look at those sorts of things as we conduct this investigation."

He said the ADF would look at how the US army responds to similar incidents.

"But let me stress we have been in Afghanistan on this mission for six years.

"We've worked with thousands and thousands of Afghans through those six years right from the outset, and this is the first incident we've had of this nature."

He said the name and other details of the rogue soldier were known and he was being hunted.

"This was not an imposter. This was someone who had been in the ANA for a while and I would characterise him as a rogue soldier," Air Chief Marshal Houston said.

He denied tensions had risen between Australian troops and Afghan soldiers over the incident.

"It was the Afghan National Army that mounted the security patrol immediately after the incident and it was an Afghan soldier that fired at the individual as he absconded.

"I think all of that is going to assist in maintaining the relationship at the patrol base."

Air Chief Marshal Houston said the dead soldier had been in the army for seven years, had served in East Timor and started his rotation in Afghanistan last November.

"I'm told he was a loyal, reliable and very trusted member of his unit. Though he was quiet and reserved, he enjoyed a joke with his mates and was always the first to volunteer when work was required to be done."

He said he wants the soldier's family to know the Defence Force will be there to provide comfort and support as their loved one is laid to rest.

Chopper crash

He said the Chinook helicopter was operating in daylight along with a US helicopter and it is not clear what happened.

The American helicopter "provided immediately medivac assistance" for the soldier but he could not be saved.

He described the dead pilot as a man who had provided "sterling service" in Afghanistan.

"He had previously been deployed in East Timor and had been part of Operation Flood Assist in Queensland, coming to the assistance of his fellow Australians who found themselves in need in January."

He said another five Australian soldiers on the helicopter were evacuated to Kandahar and are all in a satisfactory condition.

"We are very eager to know if there was any enemy action involved or whether there was some other problem with the helicopter," Air Chief Marshal Houston said.

He said an accident investigation team would be deployed and if enemy action was involved, the International Security Assistance Force would be called in.

Prime Minister Julia Gillard described news of the two deaths as "heart-breaking" and offered her condolences to the families of the two men.

"The nation will be thinking of these two families today," she said.

"They will be thinking of them with warmth, they will be sending their sincerest best wishes at this incredibly difficult time for those two families and for our nation."

The deaths come a week after Defence announced the death of Sergeant Brett Wood, of the Sydney-based 2nd Commando Regiment.

Sergeant Wood was killed by an improvised explosive device and his body was flown back to Sydney's RAAF Richmond base yesterday.

A total of 26 Australian soldiers have now been killed while serving in Afghanistan.