The Scotland international sustained the injury in the opening stages of Wednesday night's defeat at Celtic Park when he was challenged by Paul Hartley, with the Bhoys man shown a yellow card.
McCulloch played on for the remainder of the game, but a scan has revealed the problem, with the injury now requiring further assessment.
Manager Walter Smith told the Daily Record: "The initial X-rays have shown there is a crack in Lee's foot but we must wait for the swelling to go down before it can be properly assessed.
"Even with a fracture it can sometimes be possible for a player to continue playing but we will have to wait to see what the doctors say when he returns for another scan."
McCulloch is certain to miss Sunday's Scottish Cup semi-final against St Johnstone.