The 17 employees of Action Against Hunger, an international relief agency, were shot at close range in August during a fierce battle between the government and Tamil Tiger rebels for the eastern town of Muttur.
All but one of the aid workers were ethnic Tamils.
International monitors of Sri Lanka's disintegrating ceasefire have implicated government troops in the massacre - a claim strongly denied by authorities.
The UN and aid agencies have pressed for an impartial investigation.
Nihal Samarakoon, a police spokesman, said that the remains of the aid workers will be transported to Colombo, the capital, where they will be re-examined as part of the Australian-led independent inquiry.
He said that other bodies may be exhumed once their families give their consent.
Meanwhile, police said on Saturday that seven civilians had been shot dead over the previous two days in northern Jaffna, long a flashpoint for violence in the near-two decade war between separatist Tamil Tiger rebels and the Sri Lankan government.