30-year-old Dean Mohared, of Woodley, Stockport is charged with perverting the course of justice and unauthorised access to computer data.
Two other men have also been charged in connection with the investigation.
18-year-old Liam Cliff, of Woodlands Road, Manchester, and 46-year-old Vincent Rossi, of Wingfield Avenue, Wilmslow are charged with perverting the course of justice.
The three will appear before Stockport Magistrates’ Court on 5 December.
Mohareb, a Football League referee, is a senior member of the FA Referees Department as national referee development manager.
He was arrested in October 2012 over allegations that he hacked into a colleague’s email account.