"We urge President Mahinda Rajapakse to launch an exhaustive criminal investigation by requesting the assistance of international experts," Paris-based RSF said in a statement.
It also said the Sri Lankan government was doing nothing to solve the case "and in fact is clearly preventing the truth from coming to light".
No arrests have been made over the killing of Wickrematunga, who was editor of the Sunday Leader and a staunch critic of the war against Tamil Tiger rebels.
"By blocking the investigation and by fostering a climate of impunity and indifference, the government has become an accomplice," RSF said.
A total of 17 journalists and media employees have been killed in Sri Lanka in the past decade and many local reporters exercise self-censorship to avoid confrontations with the authorities, according to rights groups.
Government soldiers defeated the Tigers in May 2009 after decades of fighting.