Gill has been playing with the injury since the start of the season and the 31-year-old midfielder will now undergo exploratory surgery to try to get to the bottom of the problem.
Pirates boss Mark McGhee told the club's official website: "The scan was not conclusive, so they will do a little procedure to look inside to see what is going on.
"It is four to six weeks at this stage, but if it is anything worse than simply needing a bit of a clean out then it could be anything up to 12 weeks.
"He has been playing and training through the problem, and occasionally missing training - although not often.
"He has been gritting his teeth and getting through it, and I think he has done pretty well and I have a lot of respect for that."