Spokeswoman Oana Lungescu said NATO and Afghan authorities are investigating Saturday's bombing of a compound in Helmand province, which Karzai said left 14 civilians dead, but made clear there would be no halt to such operations.
"There will be continued coordination with Afghan security forces on such operations. They are necessary, they continue to be necessary, but they are conducted in coordination and together with Afghan security forces," she told reporters.
The spokeswoman said that NATO commanders "make every effort to ensure there is no loss of innocent life".
Afghan authorities say 11 of those killed on Saturday were children.
"These operations are conducted together with Afghan forces and I think in 85 percent of such operations no shot is fired," Lungescu said, adding that for NATO "every life is precious so we regret the loss of any life."
"We continue to take very seriously concerns expressed by President Karzai," she added.
Karzai warned Tuesday that the foreign mission in Afghanistan risks becoming an "occupying force" if air strikes continue to cause civilian casualties, and he reiterated that bombing the homes of ordinary Afghans was now "banned."
NATO's International Security Assistance Force put the death toll in the incident in southern Helmand at nine and has apologised. It said the strike was carried out after insurgents who had earlier killed a patrolling marine hid in a compound and carried on firing.
Western military figures say that hiding among civilians is a regular Taliban tactic when they are being pursued by international forces.
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