The Iron, relegated to League Two last season, took up a 12-month option on Duffy's contract this summer.
The 27-year-old is the subject of a written bid from Rovers, but Scunthorpe boss Brian Laws insists the Championship club's valuation of the player is "way below" his.
"We've received an offer from Doncaster, which was well under the valuation which we are expecting," Laws told the Scunthorpe Telegraph.
"We're not in a position where we're going to allow players to leave for next to nothing. We've paid money for him and we at least expect that back.
"No doubt about it, he had his best year since he's been at the football club last season. He's improved while he's been there and if someone improves you expect to get better money back.
"Doncaster's valuation was way below our's."