Kent, 21, will have an operation after rupturing ankle ligaments in the League Two defeat at Accrington on Saturday.
Johnstone, 27, has had surgery to repair a tear in his knee cartilage.
Defender Tom Eastman, 25, will also be out for several weeks with torn ankle ligaments, but he is expected to return before the end of the season.
Colchester United defender Frankie Kent and forward Denny Johnstone have been ruled out for the rest of the season because of injuries.