The commander, identified as Dur Mohammad, shot and killed five police officers under his command, The New York Times reported.
Mohammad fled the scene after the attack, said Gen. Abdul Aziz Ghairat, the provincial police chief.
Ghairat did not offer a motive but said Mohammad had ties to the Taliban in the area.
Also Monday, an Afghan policewoman shot and killed a U.S. adviser Monday in an apparent insider attack at the Kabul police headquarters, sources told The Washington Post.
The woman was arrested shortly after the incident, the Post reported, quoting U.S. and Afghan sources. It was believed to be the first such insider attack by a woman.
The victim was a contractor working as police adviser, CNN reported.
"He was shot in his heart and died very quickly afterwards in the hospital," the Post quoted an official as saying.
NATO's International Security Assistance Force confirmed the shooting and spokesman Charlie Stadlander said the attacker was a woman.
"A civilian police adviser was shot and killed this morning by a suspected member of Afghan uniformed police outside the Kabul police headquarters," Stadtlander said.
The Post quoted an Afghan police official as saying the attacker is one of the 1,850 female police officers trained in the country since 2002. The victim had previously worked in the Afghan Interior Ministry, which is in charge of the Afghan police.
The arrested woman officer was being questioned to determine the motive for the shooting.
Insider attacks, either by members of the Afghan security forces or by insurgents posing as members, have become a major threat for the U.S. and NATO forces in the country with more than 50 coalition forces already killed in such attacks this year.
Separately, a member of the ISAF was killed in an insurgent attack in eastern Afghanistan but his nationality was not immediately known, CNN said.
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