The official says one of the men was decapitated and the other was shot. Both were killed in a tribal region in northwestern Pakistan, notorious as a hideout for al Qaeda and the Taliban.
The slain man's body, which villagers spotted early Sunday, was dumped by the side of a road on the outskirts of Miran Shah, the main town in North Waziristan tribal region, the official said on condition of anonymity because he was not authorized to make media comments.
A note written in the locally spoken Pashto language that was found with the body identified the man as Habibur Rehman of Zurmat tribe from Afghanistan's Ghazni province, the official said.
The note claimed the man was getting $200 a month for spying for the United States.
The man's head, hands and legs had been severed. And the note warned that no one should perform a funeral for him.
The other man was found shot to death near a bazaar.
Militants are blamed for attacking people suspected of spying for U.S. and Pakistani authorities in the region, which borders Afghanistan, and where al Qaeda- and Taliban-linked fighters operate.
Scores of people — including Afghan refugees and Pakistani tribesmen and clerics — have been killed in such attacks in the region in recent years.
Pakistan has deployed some 90,000 troops to its regions bordering Afghanistan, including North Waziristan, to track down militants.
But U.S. and Afghan officials say militants still have bases in Pakistani territories from where they orchestrate attacks inside Afghanistan.
Violence has increased in the Pakistani region in recent weeks and militants, who renounced a peace deal with authorities last month, have since then staged almost daily attacks on security forces.
Pakistan army helicopters strafed a suspected militant facility late Saturday west of Miran Shah, but there were no reports of casualties, another intelligence official said on condition of anonymity because he was unauthorized to make media comments.
The facility included a residential area and an arms storing facility, located in a rugged area about 24 miles from Miran Shah, he said.
Military officials were not immediately available for any confirmation of the reported raid.