The Muslim Council of Britain says it is to write to the BBC's Editorial Complaints Unit about an edition of the current affairs programme Panorama.
The Muslim Council of Britain says its complaint was not addressed
The announcement came after the editor of Panorama rejected an MCB objection that the programme was "deeply unfair".
Panorama had quoted one of its founders as saying the body was "in denial" about extreme views among its members.
The MCB said it was at the "forefront" of criticising extremism and it was "not satisfied" with the response.
In its original complaint, the MCB claimed editors "deliberately garbled" interviews with Muslims in the programme.
Panorama editor Mike Robinson has described the suggestion as 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.
MCB spokesman Inayat Bunglawala told the BBC News website: "We are not at all satisfied with Mike Robinson's response and will be taking this up further by writing to the BBC Editorial Complaints Unit."
He said Panorama appeared to have reached a conclusion without giving a "rounded account".
"The Muslim Council of Britain has been at the forefront of challenging and criticising any form of extremist behaviour in this country," he said.
He said the MCB sent a letter to every mosque and Islamic institution in the UK after the Madrid bombings urging full co-operation with any subsequent investigations.
It had also distributed 500,000 copies of a pocket guide in conjunction with the Association of Chief Police Officers in which the government's anti-terrorism hotline number was detailed.
In Panorama's letter to the MCB it states "the programme team was well aware of the leaflets and letter" but neither "addressed the issues and questions which we raised in the programme".
The BBC said Panorama would not be commenting on the latest MCB announcement.
"The editor of Panorama has issued a detailed and considered response to the MCB's complaint," a BBC spokesman said.
"Panorama would be the first to point out that the MCB are entitled to pursue the matter through the BBC's complaints procedure."