Two of the three Australian soldiers being prosecuted over a deadly raid in Afghanistan have strenuously denied the charges levelled against them.

The Director of Military Prosecutions says three former members of the Special Operations Task Group have been charged with a number of offences relating to a February 2009 raid which left six people dead, including five children, in Uruzgan province.

One soldier is facing a manslaughter charge, a second has been charged with failing to comply with a lawful general order, and a third, currently travelling overseas, will be formally charged when he returns to Australia.

The charges relate to an incident on February 12, 2009, when six Afghans were killed during a raid targeting an insurgent leader in Uruzgan province. Five children were killed in the raid along with a suspected Taliban insurgent. Two more children and two adults were also injured.

Defence previously said the deaths occurred as the soldiers conducted clearance operations using gunfire and hand grenades.

Two of the soldiers, known only as Soldiers A and B, issued a statement late on Monday, saying they were forced to make split-second decisions when they came under fire.

They said that when the facts of the battle became public, it would be clear that decisions they took in "truly awful circumstances" would be vindicated.

"We will strenuously defend the charges and we look forward to the opportunity of publicly clearing our reputations, as well as the reputation of the Australian Defence Force," the pair said through law firm Kennedys.

Soldiers A and B also attacked the media for what they called "many cases" of inaccurate reports of the clearance operations.

They said words would never adequately express their regret that women and children were killed and injured during the incident.

They said those were the people they were risking their lives to protect.

The soldiers put the blame for the deaths at the feet of the enemy, saying it should not be forgotten the casualties were ultimately caused by the "callous and reckless" act of an insurgent, who chose to fire upon them at close range from within a room known to contain women and children.

A Defence spokesman says two of the soldiers are reservists and one is a regular member of the Army.

The decision to press charges came after the ADF carried out an operational investigation and referred the incident to the Director of Military Prosecutions.

Australia Defence Association spokesman Neil James says the charges are not unexpected.

"This needs to be cleared in an open court," he said.

"If the charges aren't proferred, then allegations will remain against these soldiers and against the Army forever, as we've seen over years with many scurrilous allegations about previous wars."

Prime Minister Julia Gillard said the matter would not affect how operations are conducted in Afghanistan.

"Our rules of engagement in Afghanistan and our mission there remain the same," she said.

"Obviously there is a process through the military prosecutor and military legal processes. I don't want to be seen to prejudge matters involving these individuals. That wouldn't be appropriate."

The matters will be heard before a service tribunal which is not expected to begin until early next year. The maximum penalty for manslaughter is 20 years.

The Chief of Defence Force, Air Chief Marshal Angus Houston, says the soldiers will receive support services including but not limited to medical, psychological, legal, chaplaincy and welfare support.

"Consistent with the presumption of innocence, these members will receive the full support of the Australian Defence Force," Air Chief Marshal Houston said.