A new book from journalists Tom Lyons and Brian Carey revealed the Fianna Fail leader and Mr FitzPatrick met for a game of golf in Wicklow two years ago, but Mr Cowen rejected allegations he had prior knowledge of the bank's problems.
"I want to take this opportunity to utterly refute any suggestions of impropriety on my part arising out of the recent publication of a book about Sean FitzPatrick," he said in a statement. "There was nothing untoward, no hidden or secret agenda."
Mr Cowen has faced calls from opposition politicians to reveal precisely what was discussed at the golf outing and in a phone call between the pair on St Patrick's Day 2008, but claimed he was unaware of the "exact scale" of Anglo's impending crisis.
Anglo was taken into state ownership in January 2009 and is the largest contributor of assets to the National Asset Management Agency, Ireland's 'bad bank'.
By Claire Archer