Bojinov, who cost £6million from Fiorentina last summer, was expected to start the season almost a year after badly damaging his knee against Manchester United, but he is struggling for full fitness.
Hughes said: "He is a little bit behind the group because he hasn't been able to join in the sessions.
"He has been out for a long, long time and he is suffering from a knock-on from the knee injury. We are aware that he will have setbacks along the way. His body is compensating, and he needs to get more base strength."