The sources said the gunmen ambushed the commander's vehicle near the Darga Mandi area in Ghulam Khan district in North Waziristan.
The Threek-i-Taliban Pakistan, or TTP, had not confirmed the killing of the commander, who had been the group's interim chief after Hakeemullah Mehsud died in a drone strike in November. The group finally picked Mullah Fazlullah as its leader.
Dawn said the commander belonged to the Khichi sub-tribe of Bhittani in South Waziristan.
Details of the shooting were not immediately available.
Geo News said the gunmen escaped after their attack.
China's Xinhua News Agency said no group had claimed responsibility for the shootings.
The attack came as peace talks between the TTP and Pakistani government negotiators remain suspended since last week because of a sharp escalation in violence by militants.
The talks were initiated by the government of Prime Minister Nawaz Sharif in a last-chance effort to end seven years of terrorist violence that has killed hundreds of people.
After the peace talks began, violence continued, including a Feb. 13 blast in Karachi that killed 13 policemen, and the Feb. 16 killing of 23 abducted paramilitary soldiers claimed by a faction of the Taliban in Mohmand tribal agency.
Government negotiators informed Sharif that continuing the talks would be meaningless unless the banned militant group immediately stopped its violence.
Pakistani military planes have recently been making airstrikes against suspected Taliban hideouts in North Waziristan. The militaary says more than two dozen suspected militants were killed.