Kompany was appointed as player-manager before the start of the season although he is yet to complete his coaching course.
Belgium FA rules stipulate that managers of all top-flight clubs hold a UEFA Pro License to be able to lead from the dugout.
"The club violated the regulations for a long time and despite that it being against the rules did not hesitate to publicly unveil a coach without a diploma," the associations licensing committee said in a statement.
Anderlecht tried to argue out their case by insisting Simon Davies, a former coaching staff at Manchester City who followed Kompany to Belgium, was the head coach.
The Belgium FA however refuted those claims by pointing to Anderlecht’s own media statements and unveiling video clips as evidence.
Anderlecht have further added to the confusion as to who is really in charge by naming Frank Vercauteren as head coach while demoting Davies to an assistant manager.
Kompany exited Manchester City at the end of last season to become player-manager at his boyhood club but so far his tenure has been anything but fruitful.
Anderlecht, who are Belgium’s most successful club with 34 league titles, have won just two out of 10 league games all season.
Such is Anderlecht’s poor form; they lie 13th in the 16-team league despite recruiting the likes of Samir Nasri, Nacer Chadli and Kemar Roofe over the summer.
