The governor of Shindand district in Herat, where the operation took place, said three civilians were killed and three children were wounded when insurgents used a civilian house for cover during the fighting.
NATO rejected claims that the operations had caused civilian casualties, saying the security force "protected several women and children present in the compounds, and no civilians were harmed during the operation."
The alliance said the operation was conducted because the area was "associated with a leading (bomb) facilitator."
In the southern province of Zabul, a woman was accidentally killed when another joint operation by Afghan and international forces used explosives to enter a compound in search of a Taliban district commander, NATO said.
In the same province, a district chief said a roadside bomb struck a civilian vehicle, killing three people and wounding two others.
Separately, the alliance announced the deaths of two U.S. service members and an American civilian contractor in two explosions Friday in southern and eastern Afghanistan.
One U.S. service member was killed by a roadside bomb in southern Afghanistan, while the other troop and the contractor died in a separate bomb attack in eastern Afghanistan, NATO said.
No further details were released about the deaths, which bring the total number of U.S. service members killed this month to eight.