Two bodies were found Tuesday in the west of the city, Pakistan's sprawling, violent economic heart, and a piece of paper found on one suggested he was missing journalist Haji Abdul Razzaq Baluch.
But the body, which bore torture marks, was so disfigured that relatives needed several visits to the mortuary to confirm the identity.
"His face was not recognisable but his arms and feet made us recognise his body," Saeeda Sarbazi, Razzaq's sister, told AFP.
Family sources said he was abducted in part of Lyari Town, the district of Karachi worst affected by the ethnic and political gang warfare that plagues the city.
Sindh provincial information minister Sharjeel Memon told AFP authorities were "trying to collect information" on the case.
The southwestern province of Baluchistan is one of Pakistan's most deprived areas. Separatist rebels have been fighting since 2004 for autonomy and a greater share of oil, gas and mineral deposits in the southwestern province.
Earlier this year the media campaign group Reporters Without Borders wrote to the Pakistani government urging it to end "abuses" by state intelligence agencies accused of abducting and killing journalists.
