The 34-year-old manager of the firm in Chiba prefecture east of Tokyo found the two sealed boxes outside the door of his office yesterday morning, police said.
He called the emergency services after opening one of the boxes and discovering a human skull inside, a local police spokesman said.
The other box was found to contain a number of bones of varying lengths and sizes, believed to be from the same body.
Officers are investigating the incident in the town of Onjuku, and trying to establish where the bones came from.