The midfielder has ankle ligament damage which he picked during the 3-0 defeat at Reading on Monday and is in London today having an operation to repair the damage.
Speaking to the CT, Coleman said about Deegan: "The ligament came off his bone and it speaks volumes for the lad that he played the rest of the game and I don't know how he managed that.
"He has got to have an op and it is a shame as he and Jon Stead cover a lot of ground for us and get through a big workload. With the position we are in, we are looking for players like that and we have lost him and Steady until the start of next season.
"Gary did a bit better this year than I expected. He has been finding his feet and getting stronger and stronger. "It is always nice when you go to a new club to get your first pre-season under your belt and it is hard to join in midway through. I have done that myself but when you get that pre-season in, if it is a good one, then you usually stay free of injury. And more often than not, you see a better second season for the player and I am hoping that is the case with Gary.
"But at the moment, we're looking at making sure we get him over this little hiccup and get him back."