The Iron lost £1.95million in the financial year which ended in June, and Wharton has loaned the club £2m in anticipation of a further loss this campaign.
"These are shameful accounts really and I do apologise but it has been a tough time these last two or three years and we have to work extremely hard to see our way through it, but I'm sure we will do," said Wharton.
Wharton is planning to step aside at the end of this season, and said he the directors were "exploring all possibilities" for the future of the club.
"When I retire as a chairman, it will be up the board to elect a new chairman and that's fairly straightforward," he added.
"The board, and myself included, are looking for people to add to the board as we speak, and if there is anyone who knows anybody who might have an interest I'd urge them to put themselves forward. We'd be pleased to hear from them."
The majority of questions were asked by the Iron Trust, with the biggest chunk of time spent discussing the club's response to the EPPP youth development scheme adopted by the Football League.
The Iron spend £105,000 a season on the academy system, and receive £210,000 in central funding because of this.
Keith Wagstaff, the director who oversees the youth scheme, said that overall there were more benefits than negatives for Scunthorpe United.
"It is very complicated, but long-term it is going to improve our footballers," he said.
"There are some positives and some negatives, more positives I think as we are now involved more in coaching the boys.
"Over the past three years we have seen a big improvement of our U16s, and in the U9/10/11 ages we are beginning to see big changes."
Wagstaff explained that although there is now a set compensation should players move to another club before signing as a trainee, any player going on to sign a youth contract would go in to the current system where the club would be able to negotiate any transfer fee.
"We can say now if a player wants to move up to 16, but it depends largely on the parents," added Wagstaff.
"At 16 the player will go on to a youth contract so is not relevant, but if we lose someone before that we might not get as much as we want."
Wharton described the improvement of facilities at Glanford Park such as toilets as an "ongoing process".
He also explained the chairman of the Football League had written to all 72 clubs apologising for the problems which have affected club's official websites this season.
A new company won the contract to provide the technical support from this summer, but at times the club's media manager has been unable to add stories.
David Beeby, the club's general manager, also revealed that the club's playing budget is the 12th highest in League One. Last season it was the 10th highest.
Rex Garton and Jason Oxenforth were both re-elected as directors, John Godfrey as president and the vice-preresidents backed en bloc. All were elected unanimously.