The three women were killed during the shooting, Nato said.
Nato had earlier said its troops had found the women already killed, bound and gagged, but later acknowledged that this was untrue.
Troops who visited the scene had made the mistake after seeing the bodies bound in preparation for burial, it said.
Two newspaper reports, however, said on Monday that the foreign troops involved in the shooting were members of US special forces who had tried to cover up the deaths by removing bullets from the bodies.
Britian's The Times cited Afghan investigators as saying the victims' wounds had been washed with alcoholafter the bullets were removed, presumably to erase forensic evidence.
A New York Times report, meanwhile, said investigators found signs of evidence tamperingat the scene, including the removal of bullets from walls near where the women were killed.
Night raid restrictions
Reducing the civilian deaths caused by his troops has been a central focus of General Stanley McChrystal, the commander of Nato and US forces, who promised a new strategy focusing on the protection of Afghans after he took up the post in the middle of 2009.
In March, McChrystal issued new orders to his troops calling for restrictions on night raids, though not an outright ban, saying that despite their tactical value they had come at a "steep cost in terms of perceptions of the Afghan people".
The United Nations says foreign and Afghan government troops killed 25 per cent fewer civilians last year than in 2008.
But civilian deaths reportedly rose overall, because the number killed by Taliban fighters rose by 40 per cent, making last year the deadliest year for Afghan civilians.
The admission came as Hamid Karzai, the Afghan president, sought to rally public support for an upcoming military operation in Kandahar.
He told tribal leaders on Sunday that US and Nato troops would push into Taliban-controlled areas only after consultations with community leaders.