Officers were called just before 2pm following the grisly find.
Police said the bus station site off Winding Road - currently under development to create a new multi-million pound facility - was a burial ground before the bus station was built.
Officers are now working with the coroner's office about the discovery.
A spokesperson for West Yorkshire Police said: "Police were called shortly before 2pm yesterday to a report of the discovery of what were believed to be human bones at the Halifax Bus Station redevelopment site.
"The site was previously a burial ground prior to the construction of the bus station.
"Officers attended at the scene and are liaising with the coroner’s office."