The 26-year-old was one of 19 riders caught up in the incident, with five taken to hospital, although the other four's injuries are not serious.
The crash happened near Verviers and the stage was abandoned.
In March, Antoine Demoitie of Belgium died after being hit by a motorbike during the Gent-Wevelgem one-day race.
Race spokesman Chris Vannoppen confirmed Broeckx is in a coma and his Lotto-Soudal team added that he had been taken to a nearby hospital in Aachen, Germany.
Cycling's governing body said: "The UCI has recently introduced strict new rules governing the conduct of motorcycle riders in races and we will be looking very closely at what happened today to determine whether those rules were respected."
Belgian rider Stig Broeckx is in a coma after a crash involving two race motorbikes during Saturday's third stage of the Tour of Belgium.