Lasantha Wickrematunge ran the Sunday Leader, which was frequently critical of the government of President Mahinda Rajapaksa, who was in power then.
In January 2009 he 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.
His death 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.
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 Wickrematunge's murder.
In July, a military intelligence officer became the first person to be arrested in connection with his death.
Then earlier this month, a judge gave permission for his body to be exhumed, because of conflicting reports from initial autopsies. His grave has been under guard since then.