MAZAR-I-SHARIF, Afghanistan — A political crisis is brewing in northern Afghanistan, where government forces on Wednesday opened fire on supporters of a powerful militia commander as they were protesting his arrest.

The commander, Nizamuddin Qaisari, is a district police chief in the Taliban-besieged province of Faryab. He is also a close ally of the exiled vice president Gen. Abdul Rashid Dostum, who has fallen out with the Afghan president.

Mr. Qaisari is the de facto commander of General Dostum’s militia in Faryab and, like his boss, has increasingly clashed with Afghan civilian and military officials over a lack of security in the ethnic Uzbek stronghold.

Senior Afghan officials said Mr. Qaisari’s arrest was part of a broader effort to rein in pro-government strongmen whom they accuse of abusing power and driving local residents into the arms of the insurgency. The officials also accuse these strongmen of sabotaging military operations.