The unnamed official said Noorullah Hotak was killed by gunmen Thursday afternoon, Khaama Press reported Saturday.
The commander blamed the assassination on Afghan intelligence agents.
Separately, forces with Pakistan's Frontier Corps said Saturday they had seized a huge cache of arms and ammunition during an operation on the outskirts of Quetta, Dawn News reported.
In three compounds, the paramilitary force said it found 1,650 land mines, 480 hand grenades, more than 5,500 pounds of explosive material, seven suicide jackets and other material.
Khan Wasey, a Frontier Corps spokesman, said all the weapons had been smuggled from Afghanistan.
Two suspects were arrested but later released.
In another operation near the border with Afghanistan, the Frontier Corps reported finding 23 rockets, explosives and other weapons.