'Excessive use of force'
The UN found most deaths attributed to pro-government forces were killed in air raids as well as search and seizure operations.
"These often involved excessive use of force, destruction to property and cultural insensitivity, particularly towards women," it said.
But it said that a change in Nato command structure had helped reduce the number of non-combatant deaths by coalition troops.
US General Stanley McChrystal, the commander of the foreign forces in Afghanistan, has made minimising civilian deaths and injuries a central tenet of his counter-insurgency strategy, ordering reduced air attacks as one way of achieving this objective.
The UN report said the change in Nato forces' command structure, "specific steps to minimise civilian casualties" and "a new tactical directive" by the force contributed to the reduction in non-combatant deaths.
Civilian casualties are a source of tension between the Afghan government of Hamid Karzai, the Afghan president, and the international forces fighting the insurgency.
Recent incidents, such as the deaths of 10 civilians including eight teenagers in eastern Kunar province in an authorised but non-military US operation, have seen Afghans take to the streets to protest against the presence of foreign troops.