For months, there have been conflicting reports about the health of 84-year old Mr Mubarak, who was sentenced in June to life in prison for failing to stop the killing of hundreds of protesters during last year's uprising.
He is the first Arab president to serve a prison sentence.
General Mohammed Ibrahim, the deputy interior minister, said Mr Mubarak will be returned to prison after treatment.
Mr Mubarak fell in the prison bathroom on Saturday.
The hospital is located in a Cairo suburb of Maadi.
Mr Mubarak's family and lawyer have urged authorities to keep him in the hospital and complained about poor prison facilities.