Belgium international Boyata was substituted in a friendly against Slavia Prague earlier this week after straining his medial knee ligament.
The news was confirmed by Celtic assistant manager Chris Davies as the team prepared to fly out to Ireland for a friendly against Shamrock Rovers on Saturday.
“It looks like a pretty bad knee injury,” Davies said.
“It’s really disappointing for Dedryck. He did really well for us for the last six months of last season and was in good form.
“We are all disappointed for him, but no doubt he will do the work he has to do in rehab and come back even stronger and better.
“The timeline we are looking at, at the minute is up to three months, but we’re always optimistic and we will see what we can do.”
Boyata’s injury could affect Celtic’s transfer plans with only Erik Sviatchenko and Jozo Simunovic fit at centre-back.
When asked whether Boyata’s injury would influence Celtic’s transfer priorities, Davies said: “With Dedryck being out that’s obviously something we are aware of now and something that we will discuss. We will see what needs to
Davies added: “Like we have said before, we want to retain the players we have got here at the minute, we are happy with what we have got. If the right player becomes available and we can do the right business for the club, then we will look at that.”