Pearson used his programme notes ahead of Wednesday night's match against Aston Villa to blast Duffen, who resigned in October, allowing Pearson to return to the role he had previously held between 2001 and 2007.
"In my personal opinion, the decisions made by Mr Duffen were extremely short-sighted and lacking in business sense and specific football knowledge," wrote Pearson.
"He seems, albeit with the advantage of hindsight, to have had no understanding of the industry, Hull City AFC or the city of Hull itself."
He went on to accuse Duffen, who led Hull into the Premier League, of "poor business sense" and a "lack of moral responsibility" while describing the money spent on agents as "morally abhorrent".
With Hull looking destined for relegation after two seasons in the top flight, there are concerns the club may be forced into administration.
Duffen, though, maintained Hull have "one of the lowest squad wage bills in the Premier League and amongst the lowest levels of debt".
He added in his statement: "The successes were not achieved through financial muscle but through partnerships, ambition, team spirit, collective positive attitude and a stubborn refusal to fail.
"I firmly believe that if those qualities remain at the club then Hull City have every chance of playing a third season in the Premier League and I wish them well."
Meanwhile, Hull were boosted today by the news Jan Vennegoor of Hesselink's CT scan showed no damage.
The Dutch striker was knocked unconscious in a collision with Richard Dunne last night, with the game being delayed for seven minutes while he was treated on the pitch.
Vennegoor of Hesselink was taken to Hull Royal Infirmary but has now been released and is recovering at home.
However, the 31-year-old will definitely be unavailable for Saturday's home match against Sunderland and is not expected to return to full training until the end of next week.
A statement on www.hullcityafc.net read: "We are pleased to report that the scan came back all clear.
"Vennegoor of Hesselink will now be monitored daily with the hope being that he will return to full training late next week."