In addition, the club's accounts - finally released this week, five months behind schedule - showed borrowings of £22 million, prompting accountants Deloitte to predict Hull will have to raise £23 million to balance their books should they be relegated, and £16m if they survive.
Related ArticlesHull dismiss Phil Brown sacking rumoursFears raised over Hull's financesHull City v Portsmouth: match previewFulham 2 Hull City 0Dean Windass retiresSport on televisionBrown remains at the club and arrived at Hull's Cottingham training ground as usual to take this morning's session, but Duffen confirmed his departure shortly afterwards.
In a statement, Duffen said: "When I succeeded Adam Pearson as chairman of Hull City Football Club in June 2007 I was very aware of the responsibility to build on his legacy.
"I articulated an intention to take the Tigers to the previously uncharted waters of the Premier League and to the eternal credit of the players and coaching staff, that seemingly ridiculous ambition was achieved 11 months later thanks to a victorious debut appearance at Wembley in the play-off final.
"The start to our maiden top-flight campaign broke all previous records for a newly promoted side and ensured that 2008 will forever be remembered as the most remarkable year in Hull City's history.
"Football is a results business and in the same way that I enjoyed the successes of the previous two seasons, so I must take ultimate responsibility for the disappointments of 2009.
"It has been a tremendous privilege to lead the Tigers on this amazing journey and I pay tribute to all the staff for their hard work and dedication as well as to the fans for their magnificent support. I am proud to have played my part and wish the club every success in the future."
Pearson yesterday resigned as chairman of football at Coca-Cola Championship side Derby County, sparking suggestions he is set to return to East Yorkshire.
Hull will reveal more regarding the future control of the club at boardroom level early next week.
"The recruitment process has commenced in respect of the appointment of a new executive chairman and a further statement in relation to this will be issued by the club on Monday 2nd November," a statement said.