Duffen stood down after pressure mounted on him and manager Phil Brown following the club's poor start to their second season in the top flight, which has seen them take just eight points from their opening 10 games.
The club's accounts are also in the red with accountants Deloitte predicting they will have to raise 23 million pounds to balance their books should they be relegated, and 16 million if they survive.
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.
"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."
There had been speculation over the future of both Duffen and manager Phil Brown in recent days, with the club taking the unusual step on Wednesday of denying reports that Brown had been sacked.
Hull issued a statement after several leading bookmakers stopped taking bets on Brown being the next Premier League manager to lose his job.
The Tigers' next match sees them away to Burnley on Saturday.