Lasantha Wickrematunge edited the Sunday Leader, which was critical of then President Mahinda Rajapaksa.
He said before his 2009 murder that the government would kill him. The Rajapaksa government denied the claim.
A new post-mortem will be held to establish cause of death. In July, a military intelligence official was arrested in connection with the murder.
Lasantha Wickrematunge’s killing came at a time of intense restrictions on the media in Sri Lanka.
The Sunday Leader had accused the government and the military of rights abuses during their fight against the Tamil Tiger separatist movement.
In January 2009 the editor had written an editorial saying he believed he would be killed by the government and that an inquiry would come to nothing.
He was killed by unidentified attackers in Colombo three days later.
After his surprise win in elections in 2014, the new President, Maithripala Sirisena, vowed to reform Sri Lanka’s treatment of the media and to reopen the investigation into Mr. Wickrematunge’s murder.
The military intelligence officer held in July was the first person to be arrested in the case.
Earlier this month, a judge gave permission for the editor’s body to be exhumed, because of conflicting reports from initial post-mortem examinations. His grave has been under guard since then.
Journalist Mandana Ismail Abeywickrama, who was a close friend of the editor, was nominated by his family to witness the exhumation.
“I had to identify the body – it was one of the most difficult things I have done in my life,” she told BBC Sinhala’s Azzam Ameen.