The 34-year-old has not played since mid-April when he suffered a medial ligament injury while on loan with Rovers from Scunthorpe United.
He joined on a permanent deal in the summer but has yet to feature, despite sporadic returns to first team training.
And he went under the knife last week in a bid to rid of the troublesome problem.
"He's had to have an operation on Wednesday so he'll be out for another 16 weeks," Ferguson said.
"That's a nightmare. Gaz is going to be out for another four months.
"It's bad news for him because he's champing at the bit.
"But after going to see the surgeon again, he's advised us the only real solution because it hasn't got any better is an operation.
"We'll just have to make sure we pull the reins on Gaz because I know what he's like, he'll want to get back before then.
"It's unfortunate for him because he's a great lad and he just wants to play football."
Ferguson revealed that McSheffrey missed some rehabilitation time in the summer as he took part in a coaching course.
But he insists the veteran forward was still expected to return to fitness in time for the start of the season.
He said: "The initial situation was that he did his medial ligaments.
"In the summer, he went on a coaching course because he's doing his badges, which I encourage.
"It's something, once he gets on his feet again, that we might get him doing a bit of coaching with the kids here.
"That played a little bit into his rehab time.
"But then he was fine and we fully expected him to be back for pre-season.
"He just wasn't there and then he had a couple of injections to take away the swelling in his knee.
"Sometimes, what we've been told, the only way to cure it is the operation.
"It just won't cure by itself and the joint at the bottom of his knee just wasn't connecting.
"The surgeon says he's getting it more often now, with footballers in particular, where the only way of doing it after trying everything up to that point is operating.
"I suppose you could say we could have operated straight away but we thought it would heal naturally.
"He got injured in March and he probably won't be back until next February or March time."