Steve Wharton, the club's chairman, revealed the losses in an interview with the Scuntorpe Telegraph which was published on Thursday.
"Money's very tight. We suffered a large loss last year, and we're heading for a large loss again this year," he said, when asked if money would be made available for further loan signings.
"Unless someone comes in to put investment into the club we're certainly spending far more than we ought to be."
The predicted loss will be in stark contrast to this time last year, when the accounts for 2010/11 showed a profit of £1.4million thanks to the sales of Gary Hooper, Martyn Woolford and Jonathan Forte. Without those sales the club would have lost almost a quarter of a million.
The club's wage bill - for all employees - was £5.5m, including social security costs.
Wharton accompanied those accounts with a warning that relegation to League One would be accompanied with a bid "to reduce our operating costs over the next few years, unless we can return to the higher league".
He is currently seeking to step aside as chairman, but says he has made no progress in finding his replacement.