The body of Khalid Khawaja, a former Inter-Services Intelligence (ISI) officer, was dumped in Mir Ali town in North Waziristan, an intelligence official said.
A note attached to his body accused him of spying for the United States and killing innocent people during the 2007 government siege of radical Islamists holed up in a mosque in the capital Islamabad, the official added.
"Khalid Khawaja received two bullets, one to the head and second to his chest," the intelligence official told AFP on condition of anonymity. Another local intelligence official confirmed the incident.
Khawaja went missing with another former military officer and a journalist in March while travelling to North Waziristan, a stronghold of Afghan Taliban, al Qaeda and foreign Islamist militants.
A previously unknown group calling themselves Asian Tigers claimed to have kidnapped the group and sent a video of Khawaja to the media.
An email purportedly sent by the faction on Friday said they killed Khawaja because the government did accept conditions for his release. "Khalid Khwaja is no more," said a copy of the email seen by AFP.
"The ISI and government didn't take it seriously," it added.
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