Collins, 25, went under the knife on Monday after visiting a specialist.
"He was in London on Monday seeing the specialists and they all felt that the best thing for him was to have the operation," Iron manager Alan Knill told the club's official website.
"Which he did and now we are looking at three to six months recovery. He has not made many starts and we have not seen him on the pitch.
"We all had him down as being back for pre-season, so it's a big blow for him more than anyone."
Former Iron manager Nigel Adkins brought Collins to the club in 2010, but he has managed just 39 appearances in an injury-hit two seasons.
He is contracted to the club until the end of next season.