Dean Mohareb, 29, of Stockport, was due to officiate at Tuesday's Championship game between Barnsley and Peterborough but was stood down.
Mohareb is a senior member of the Football Association's Referees Department in his role as national referee development manager. It is understood the arrest was prompted by claims he hacked into a colleague's email account.
A spokesman for Greater Manchester Police said: "On Sunday 30 September, police seized a number of electrical items as part of an investigation into computer hacking and the dissemination of private information.
"A 29-year-old man was arrested on suspicion of unauthorised access to computer material/data, under section 1 of the Misuse of Computers Act 1990.
"The man has since been bailed until November 26."
Mohareb's job as national referee development manager includes handling sensitive information on a regular basis, including child protection issues, according to a report in The Guardian.
The report adds that police are investigating the hacking of personal and work email accounts belonging to Janie Frampton, the FA's former national referee manager for education and training.
Frampton's emails were leaked to the press, from a single email address, over an extended period. The stories arising from those emails included her allegedly offering FA Cup tickets to a flight steward in return for an upgrade.
Frampton was dismissed after an internal investigation, but is challenging her dismissal on procedural grounds.