When interviewed by Jeremy Paxman Flowers accused the Mail on Sunday as being "pseudo-facist" and a purveyor of "fiction" following stories of his drug taking whilst he was in the top job at the Co-op Bank.
He made his allegations after the paper had obtained video footage of him allegedly buying crystal meth and cocaine in the build up to a select committee he attended last year.
In a leader column the Mail on Sunday said: "The Mail on Sunday, acting quite properly in the tradition of robust journalism, played a major part in his downfall by exposing his drug abuse.
“Mr Flowers might well feel aggrieved at that. Even saints (which he is not) dislike being shown up in public.
"But why did the supposedly impartial BBC feel it was its job to sympathise with Mr Flowers, and to give him a platform for an orgy of public self-pity, combined with crude, baseless abuse of this newspaper?
"The BBC’s bias is most clearly shown by its frequent failures to pursue and interrogate those with whom it secretly sympathises. Yet it will turn like a tiger on those of whom it secretly disapproves.
"Who can forget Jeremy Paxman’s relentless interrogation of former Tory Home Secretary Michael Howard, in which he asked the same question 12 times?
"But in his encounter with Mr Flowers, Mr Paxman was transformed from tiger into purring pussycat.
"His questions were gentle lobs. He failed to rebuke Mr Flowers for blatantly flattering him with allusions to his supposed ferocity.
"Mr Paxman even laughed sycophantically at an unfunny remark about scripture, as if the two men were Oxbridge dons maundering over the port."
"The BBC simply does not deserve the great privilege of the licence fee if it cannot try harder than this to be fair."
