The Mount Lavinia Magistrate Court issued the order considering a request made by the Criminal Investigations Department, Xinhua news agency reported.
The body is expected to be exhumed on September 27, according to court orders.
Wickrematunge was the founding editor of the privately-run Sunday Leader newspaper. He was shot dead in January 2009 by a group of unidentified men in a high security zone while he drove to work in broad daylight.
He was a staunch critic of the former government of Mahinda Rajapaksa, who has denied any role in the editor's killing.
The Sri Lankan government led by Maithripala Sirisena, who came to power in January 2015, had reopened investigations into Wickremetunga's murder, pledging to arrest all those involved in the killing.
