Sir Iqbal Sacranie has complained about the Panorama special
The Muslim Council of Britain has launched a new attack on Panorama, labelling the programme "deeply unfair".
The Panorama Special - called A Question of Leadership and broadcast on Sunday - asked whether the MCB should provide a stronger lead to UK Muslims.
The reporter, John Ware, also investigated whether groups affiliated to the MCB were peddling hard-line views.
MCB Secretary General Sir Iqbal Sacranie attacked the programme before it was shown and sent a complaint to BBC Director General Mark Thompson, accusing it of following a pro-Israeli agenda.
Now the programme has been broadcast, Sir Iqbal has reiterated his disappointment with the show.
He said: "We believe John Ware's team have made a deeply unfair programme using deliberately garbled quotes in an attempt to malign the Muslim Council of Britain and with the barely concealed goal of drawing British Muslims away from being inspired in their political beliefs and actions by the faith of Islam.
"It is unfortunate that just when Britain's 1.6 million Muslims are beginning
to make progress in terms of their political participation in the mainstream,
there are those who are purposefully trying to sabotage that process."
Panorama editor issued the following statement last week, explaining the reason for the move and challenging accusations that the show is one-sided:
After the bombing attacks on London, many within the Muslim community here in Britain announced that it was now important to deal head on with the issues that may have helped motivate young British Muslim men to attack their fellow citizens.
The questions which this Sunday's Panorama examines are being raised by members of the Muslim community themselves.
They raise issues about the direction and role of the Muslim Council of Britain, and the influences on the leadership of the organisation and its affiliates.
Despite some critical comments to the contrary, it is certainly not the case that nearly all the questioning of Sir Iqbal Sacranie was about Israel.
In a wide-ranging interview with Sir Iqbal, the Secretary General of the Muslim Council of Britain, the discussion ranged from his views on the efforts to deal with extremism in some young British Muslims to the Regents Park mosque declaration.
The interview also dealt with aspects of the rhetoric of MCB affiliates and the relationship between religion and politics, as well as dealing with direct questions about suicide attacks and Sir Iqbal's views on the targeting of civilians around the world, including in Israel.
The decision to reschedule the programme and the rebilling of John Ware's Panorama on British Muslims took place some days prior to the BBC's receipt of a letter of complaint from the Muslim Council of Britain.
The programme was moved on a week to allow the production team time to complete the programme, which is now an hour-long special.
The BBC rejects completely any allegation of institutional or programme bias.
Panorama is committed to independent journalistic inquiry and completely rejects the slur that it follows an agenda determined by any interest group.
I believe that a fair-minded view of Panorama's reporting over many years would support the approach that I have described.
Next Sunday's edition will remain true to the BBC hallmark of fair and impartial reporting and we are confident that it will be a timely contribution to the present debate.
Audiences both praised and criticised the show
Audience reaction to the show has been mixed.
More than 640 people have contacted the BBC to complain that the programme portrayed Muslims and the Islamic faith in a negative light.
However, nearly 100 people have been in touch to say the programme was excellent and NewsWatch has received emails praising the show.
Alana Lewis wrote: "I despise the BNP and racism - but I do understand how radical Islam thinks and works and believe that the programme was accurate, based on many conversations that I've had in recent years with young Muslims.
"Well done! Unless these issues are properly aired then we'll all get what we deserve. There should be no room for appeasement of fanatics."
But there have also been emails dismissing the programme.
Abu Mu'min accused the BBC of "Muslim bashing", adding: "I watched Panorama with complete disgust. I think your program will only help promote further racist and Islamaphobic attacks in the UK."