Manager Lawrie Sanchez said: "He is having an operation and we expect him to be out until Christmas.
"He is captain, he is a centre forward who wins a lot in the air and is a big presence in the dressing room.
"So he is quite a big loss for us."
Sanchez is particularly disappointed to lose his captain after he had begun to work well with new strike partner David Healy.
Sanchez added: "They had an understanding going. They work for each other and David can read Brian's flick-ons.
"It is disappointing, particularly in the action of scoring his first goal of the season when it was all flowing."