Police responded to the Pleasanton Transfer Station, located at 3110 Busch Road, on reports of a found human skull.
According to police, workers removed the skull from the conveyor belt after workers spotted it amongst the recycling and told a supervisor who called police.
The Alameda County coroner's office was notified and a forensic anthropologist determined the skull belonged to a Native American, according to police.
Eric Lauritsen, operations manager at Pleasanton Garbage Service, said the skull was likely picked up by one of three recycling trucks that were in operation on Thursday, police said.
A local Native American organization has assumed control over the investigation.