"No more attacks on the homes of Afghans will be allowed," CNN reported Karzai told reporters.
The Afghan president's remarks came following a weekend airstrike in Helmand province that Afghan officials said killed up to 14 civilians, including children, CNN said.
But NATO, in its report, said the airstrike killed nine civilians. Its top commanders, including U.S. Army Gen. David Petraeus, have expressed their apologies over the incident. NATO said the airstrike was in response to the killing of a U.S. Marine and continued fighting by insurgents in that incident.
The Voice of America quoted Karzai as saying his people can no longer tolerate such NATO attacks and that its forces faced the risk of being seen as an occupying force.
The BBC reported Karzai's latest comments, described as his last warning, indicate a likely rift between him and NATO. The report said it was unclear what might happen if more such casualties occur in future NATO operations against Taliban insurgents.