40-year-old Syed Saleem Shahzad, the Pakistan bureau chief for Asia Times Online, was reported missing on Sunday evening shortly after he left his home here for a television station.
Reports earlier in the day said a body had been found near Shahzad's car at Sarai Alamghir near Jhelum town. After police informed Shahzad's family, a relative went to the site and identified the body.
Police said Shahzad's body bore marks of torture.
Shahzad's family had earlier told the media that the description provided by police did not match with that of the missing journalist.
Rights groups, including Human Rights Watch, had earlier said they believed Shahzad was in the custody of Pakistani intelligence agencies.
The International Federation of Journalists and the Pakistan Federal Union of Journalists had appealed to the Pakistani government to order security agencies to trace Shahzad.
No group claimed responsibility for the killing and Shahzad's family said he had no enmity with anyone.
Shazad had shifted from Karachi to Islamabad two years back and his reporting mostly focussed on militant groups, including banned groups and al Qaeda.
