Zemeri Bashary, an interior ministry spokesman, said that Paktiawal and his guards had gone to the police post to investigate an overnight attack by "armed men".
"Paktiawal and his men had gone there to investigate an attack on the post last night. As they entered the post, a bomb exploded which killed two officers and slightly injured Paktiawal," Bashary said.
Armed men had stormed the police post late on Tuesday and shot dead the three policemen inside, Bashary said.
He did not say who might have been responsible for the attack.
The Reuters news agency reported a police official as saying the blast was caused by a landmine.
Kabul, which is patrolled by hundreds of Afghan and international security forces, has nonetheless seen several attacks and suicide bombings.