Hayatullah Khan's body was found by villagers dumped in the tribal-dominated North Waziristan town of Mir Ali, from where he was abducted on December 5, his brother, Ahsan Ullah, told The Associated Press.
Ullah said local authorities informed him on Friday that his brother's body had been discovered.
Khan disappeared days after photographing shrapnel from a Hellfire missile allegedly fired by an American unmanned warplane to target wanted al-Qaeda figure Hamza Rabia in Mir Ali.
Khan's photograph contradicted official Pakistani claims that Egyptian-born Rabia had died in a bomb-making accident.
"We found the body of Hayatullah Khan today near Mir Ali, and we have informed his family about it," said local official Fida Mohammed.
Khan, in his mid 30s, had been handcuffed and shot once in the back, Mohammed said. It was unclear when he was killed but it appeared to be recently as his body showed no signs of decomposition, he said.
Pakistan has deployed 80,000
soldiers in the tribal provinces
The journalist's body was returned to his relatives, who took it to their village near Mir Ali, Mohammed added. Ullah refused to speculate on who may have killed his brother.
"We don't know who did it. It is the duty of the government to find out," he said.
However, he was quoted by the New York Times as blaming a Pakistani intelligence agency for the killing and vowing to avenge the death.
Ullah said his bother worked for Pakistan's Urdu-language daily Ausaf and the European Pressphoto Agency.
Sailab Mahsud, president of the Tribal Union of Journalists, vehemently condemned Khan's killing and urged the government to form an independent committee headed by a judge to probe the incident.
Masud also demanded protection for journalists working in the tribal areas, where Pakistan has deployed about 80,000 troops to flush out foreign fighters and their local supporters and where four journalists have been killed in the past year.
In January, a Pakistani government official claimed Muslim fighters may have abducted Khan.
But the New York-based Committee to Protect Journalists, citing Khan's colleagues, has said he was probably kidnapped by local authorities - a claim the government denies.
Past American missile strikes inside Pakistani territory have sparked mass protests across the deeply Islamic country and spurred criticism of Islamabad's ties with Washington.