Rovers had hoped that the 28-year-old could be fit for Saturday’s vital home clash with relegation rivals Gillingham.
But the centre back suffered an adverse reaction in a practice game at Cantley Park earlier today and his season now hangs in the balance.
"Tom unfortunately has broken down in training this morning,” said Rovers boss Gary McSheffrey.
"It was the first 11v11 situation he has played in and he’s felt something in his foot again.
"He’s in a boot at the minute and he’s having a scan in the morning so we’ll know more in 24 hours about how severe it is.”
McSheffrey added: “He felt brilliant. It’s been 12 weeks and three days since he did the injury against Shrewsbury.
"We estimated a 10-12 week [lay-off]. He’s done everything the consultant said to do. He’s ticked off all the milestones for training and he’s been out on the grass for a good few weeks with the fitness coach.
"He’s stepped into training today and the first time he probably has to do something that’s reactive to where a ball goes in a game situation, a couple of minutes in, he’s felt a little bit of a pull again in his foot.
“I’m gutted for him – the lads all had a spring in their step to have their captain back – but hopefully it’s just a nick of some scar tissue and he’ll be back in a couple of weeks but who knows. That would be the best case scenario.”
Reo Griffiths is also suffering from an achilles tendon issue and could miss this weekend’s game.
John Bostock needs match minutes and will play in an in-house friendly game next week before being considered for a return to the first team fold.
Jordy Hiwula has returned to full training this week and could return to the squad on Saturday.