The defender suffered knee ligament damage on New Year's Day and is expected to be out for at least six weeks.
Boss Micky Adams told the club's website: "John McCombe has had a scan and the news is not good.
"We need to get the swelling down and then re-scan it, but the best case scenario would mean he would be out for six weeks. The worse case, we don't know yet until the swelling goes down."
Clayton McDonald replaced McCombe against Fleetwood and could deputise once more.
Midfielder Chris Birchall has re-signed for the club but is unlikely to get international clearance in time to make his second debut.