Boyata, who has been on loan at Bolton, has suffered ankle ligament damage and has now returned to parent club Manchester City for treatment.
“Dedryck is going to be out for up to six weeks with ankle ligament damage,” said Bolton boss Owen Coyle.
“It’s a real shame, first and foremost for Dedryck because he has shown what a top player he is capable of being, and then secondly for the team and the football club.
“Part of the arrangement in the loan contract was that if an injury did occur then he would report back to Manchester City and liaise with our club doctor and the medical team here, and that is what will happen.”