The court action follows an operation in February last year to clear a compound in Uruzgan province where Australian forces believed a Taliban leader was hiding.Director of Military Prosecutions Brigadier Lyn McDade said the three "will be charged with various service offences, including manslaughter, dangerous conduct, failing to comply with a lawful general order and prejudicial conduct".
A suspected insurgent was also killed in the night raid, while four people were wounded. Two of the servicemen said they would vigorously fight the charges, which are being laid after an Australian military investigation.
"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," they said through their lawyers.
A defence department spokesman said at least one soldier will face manslaughter charges, although accusations against one of the accused have not been released as he is currently abroad.
Local media earlier said the case stems from a night-time "capture or kill" mission, involving about 30 Australian soldiers, in which troops exchanged fire with an Afghan man.
The man died, as did five children -- including two babies -- after grenades were thrown, while other women and children were injured, the Sydney Morning Herald said.
The paper said no military historians it had contacted could recall a previous case where Australian soldiers had been charged over the deaths of civilians in battle.
Civilian deaths are a sensitive issue in Afghanistan, where almost 150,000 foreign soldiers from NATO and the United States are battling a Taliban insurgency.
The United Nations reported last month that 1,271 civilians died in violence between January and June this year, with the Taliban responsible for 76 percent of the deaths