A court in the Indian state of Gujarat has ordered that samples of human remains found earlier this week be sent for DNA testing.
More than 1,000 people, mostly Muslims, died in the 2002 riots
Villagers who dug up the remains say they belong to Muslims killed during religious riots in 2002.
The investigation has been handed over to India's top detective agency, the Central Bureau of Investigation (CBI).
More than 1,000 people, mostly Muslims, were killed in the 2002 riots, although many believe the figure to be higher.
Justice CK Buch of the Gujarat High Court said samples of the remains should be collected by the CBI and state officials in the presence of the relatives of the riot victims.
He was responding to a petition by the relatives of riot victims.
The judge also said that after the DNA results were announced, the remains should be handed over to the villagers for a proper burial.
The residents of Pandarwada village, 170km (110 miles) south-west of Ahmedabad, say the bodies of riot victims were secretly buried in what they allege was a mass grave.
However, police said they were aware of the grave and those buried there had been legally accounted for.
Villagers say the grave contains 26 victims of a massacre on 1 March 2002. Eight skulls and other remains were dug up on Tuesday.
One of the relatives, Ameena Bibi, said she was satisfied with the judge's order.
"I hope we will get justice in the days to come also," she said.
A lawyer representing the Gujarat government, Kamal Trivedi, opposed the intervention of the CBI in the investigation, saying that everything had been done transparently and legally.
The Gujarat riots broke out after nearly 60 Hindus returning from the holy site of Ayodhya died when the Sabarmati Express train they were travelling on was set on fire. How the blaze started is not clear.
Gujarat police and local authorities have been heavily criticised for failing to come to the help of victims during the violence, which was among the worst in India since partition in 1947.
A judicial inquiry into the riots is still to conclude its investigation.