Central Bureau of Investigation officers and forensic experts recovered seven skulls from a mass grave in Lunavada on Wednesday.
The mass grave, where the bodies of post-Godhra riots victims are suspected to be buried, was discovered early in December.
The Gujarat high court directed the CBI on December 29 to collect skeletal samples from the grave in Panchmahal district and send it to the forensic lab in Hyderabad for DNA testing.
A 10-member CBI team headed by a deputy inspector-general and a eight-member team of forensic experts were overseeing the digging process.
The team will collect the DNA samples of the skeletal remains and compare them with that of the people who claimed they were related to the victims, the sources said.
The Gujarat government had opposed the involvement of CBI in the case and said the step will 'demoralise the police force of the state'.