Morecambe physio Dave Edge says Michael Howard could be out of action for around three months.
Howard went for a scan last week on a back problem and the results indicated a stress fracture that will require a long period of rest.
It is a major blow for the popular left-back who vowed to fight for his spot after returning to the club after a loan spell at Oxford United last season.
Howard, who also suffered a hamstring injury in pre-season, was brought into the side to face Oldham in the first round of the Johnstone's Paint Trophy but had to leave the field in the first half after feeling pain in his lower back.
Said Edge: "Although you can never be certain how long a player will be out it would be fair to say that Michael is looking at next year before being ready for the first team.''
Shrimps' skipper Jim Bentley added: "It's a huge blow for Michael. He has been compaining of a bad back for quite a while and we hope the treatment is successful.''