MacKenzie has been struggling with a hip complaint since the defeat of Notts County last Saturday and following expert advice the decision has been taken to send the centre-half for a hip arthroscopy.
The procedure will keep MacKenzie out until January. Head of sports medicine Simon Crampton told the club's official website: "Gary has had a problem within the hip joint that has been affecting his ability to perform to his high standards.
"Following a series of investigations and consultation with Professor Ernest Schilders, a world-renowned hip specialist, the decision was made that the issue needs to be rectified surgically.
"Gary will undergo the operation next Monday and then will complete an intensive rehabilitation process with our medical team and it is expected that he will be sidelined for at least 12 weeks.
"Gary is a very strong and determined individual and I know he will be putting everything into his rehab."