The clash erupted when a group of militants attacked Afghan police and U.S.-led forces in Ghazni Province overnight.
Ministry spokesman Yousuf Stanizai said two militants and a police officer were killed in the counterattack. Another three militants were wounded and captured, and three people suspected of links with the militants were detained.
The fighting was still under way by mid-morning and the area had been sealed off.
Coalition spokesman Mike Cody confirmed the clash but could not immediately provide details.
Ghazni is one of several provinces in eastern and southern Afghanistan that have experienced regular attacks by suspected Taliban and their Islamic allies.