The editor of BBC current affairs show Panorama has rejected complaints from the Muslim Council of Britain (MCB) who said a programme was "deeply unfair".
The Muslim Council of Britain's Sir Iqbal Sacranie attacked the show
The MCB complained after Panorama quoted one of its founders as saying the body was "in denial" about extreme views that prevail among its members.
The group claimed editors "deliberately garbled" interviews with Muslims.
But Panorama editor Mike Robinson has now said it was an "unwarranted and wildly inaccurate attack" on the show.
"I have found there to be no truth in your claims that this programme was dishonestly presented, maliciously motivated or Islamophobic," he wrote to the MCB.
"These are extremely serious allegations to make in the face of so much evidence to the contrary - they are simply not true."
The programme was meant to "reflect, inform and generate" debate in the Muslim community and wider population, which was "long overdue", he said.
The MCB, the UK's most powerful Islamic body, is an umbrella organisation of about 400 mosques and other Islamic groups that is seen as representing mainstream Muslim opinion.
Mehbood Kantharia, a former member of the MCB's central working committee, said they could not be "really forthright about wanting to do something about the kind of extremism that prevails".
Panorama reporter John Ware presented the investigation
Panorama reporter John Ware also found groups affiliated to the MCB promoting anti-Semitic views, the belief that Islam was a superior ideology to secular British values and the view that Christians and Jews were conspiring to undermine Islam.
MCB secretary general Sir Iqbal Sacranie complained the show was "purposefully trying to sabotage" the progress Muslims were making in the political mainstream.
"John Ware's team have made a deeply unfair programme using deliberately garbled quotes in an attempt to malign the Muslim Council of Britain," he said.