First division referee George Nicolaou, 41, was unhurt after the early morning explosion outside his home in Zakaki near the coastal town of Larnaca.
But Charalambos Skapoullis, head of the Cyprus Referees Association, told state radio Nicolaou "was in shock and troubled" by the incident.
"This is totally unacceptable. The referee has not been involved in any games that prompted any sort of reaction from teams or fans, so this attack is also puzzling," he said.
The Cyprus Football Association said such "terror" tactics "harm our football family, as well as society in general".
In January 2015, the CFA postponed all fixtures for a week when match officials staged a walk-out following a bombing outside the home of a referee's mother.
And in March 2014, referees went on strike after a bomb was planted under the car of top referee Leontios Trattos.
Whistleblower Marios Panayi last year alleged that some of his refereeing colleagues were deciding the outcomes of games with incorrect calls ordered by senior football officials.
Some football fixtures have been also flagged as "possibly rigged" after suspicious betting activity.
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