The documentary, 'A Question of Leadership', by John Ware said groups connected to the Muslim Council of Britain, which has positioned itself as the voice of moderate Muslims, were spreading hard-line religious views.
The BBC said it had received 91 calls and emails from viewers complaining about the programme.
Just two examples from the BBC website gauge how angry and upset British Muslims were by the film.
"How can the BBC justify presenting a distorted view and be responsible for creating an environment of hatred against decent and law abiding Muslims?" Mohammed asked.
"The BBC is showing something which in my opinion is blasphemy. I am deeply hurt by Panorama. I don't know whether there is any limit to what to show on national, state-run, people-funded TV .When a significant proportion of people in the UK is Muslim, is it fair to hurt someone's religious faith?" Dr Arifur Rahman, from Newport, added.
However, others praised the programme for uncovering the mixed messages that the MCB was communicating.
"A superb programme. MCB and MAB have said one thing on camera and another off it. That is a shame and these organisations must come out against terrorism lest they be seen to be walking hand in hand with them," said Alistair from London.
"Bloody brilliant, the presenter hit the nail on the head about how the Saudis fund their own translations of the Quran and are spreading books which are basically full of their own hardline and false translation of Islam," Saadia from Birmingham said.
A BBC spokeswoman defended the film, saying: "We have every confidence the Panorama report was fair and impartial."
The MCB has also retaliated with secretary-general Sir Iqbal Sacranie calling the programme "deeply unfair" and "purposefully trying to sabotage Muslim's progress in mainstream political participation."
'Panorama - A Question of Leadership' was watched by an average 1.9m viewers from 10.15pm on BBC One last night.
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