Channel 4's Aaqil Ahmed will be only second non-Christian to hold head of religion role in BBC's history.

The BBC is to have its first Muslim head of religious programming, after confirming that the Channel 4 executive Aaqil Ahmed is to take over the role.

Ahmed's appointment marks only the second time in the BBC's 87-year history that a non-Christian has been appointed to the position, following the agnostic Alan Bookbinder in 2001.

The move is likely to be controversial with some – the Archbishop of Canterbury, Dr Rowan Williams, was reported to have raised concerns with the BBC director general Mark Thompson that the "Christian voice is being sidelined" after Ahmed was first connected to the role last month.

A spokeswoman for the Archbishop of Canterbury, who is currently in Jamaica, declined to comment. However, the Bishop of Manchester, the Rt Revd Nigel McCulloch, said last night: "Aaqil Ahmed comes to the post with a good reputation. At a time when the BBC's coverage of religion caused some disquiet, the Church of England will be watching how the future of religion and ethics develops."

Ahmed, commissioning editor for religion and multicultural programmes at Channel 4, will take up a new joint role at the BBC: head of religion and ethics and commissioning editor for TV religion.

While at Channel 4, he commissioned a range of programming including Christianity: A History, The Qur'an and the Bafta-winning Saving Africa's Witch Children. Before joining Channel 4 in 2003, he was deputy head of ********aries in the BBC's religion department.

The BBC has also appointed Christine Morgan as a new separate head of religion radio. A BBC spokesman declined to comment on her religion.

The BBC said the appointment of Morgan, who has been executive producer of BBC radio religion and ethics since 2004, responsible for all religious programmes on Radio 2, Radio 3 and Radio 4, was "another measure to strengthen the BBC's religious programmes".

A BBC spokesman said the corporation appointed individuals "on the basis of talent and suitability to the role, regardless of their faith or background".

The two new appointments – part of a new management structure for the BBC Knowledge department – replace the previous combined head of religion and ethics role overseeing output on both TV and radio, which was held by the Methodist preacher Michael Wakelin.

As part of the new BBC Knowledge structure, four other commissioners have been appointed. Mark Bell, currently commissioning editor for non-in house specialist factual, will become commissioning editor for arts.

Charlotte Moore has been confirmed as commissioning editor for ********aries after acting in the role. Kim Shillinglaw, currently creative executive producer for BBC London factual, becomes commissioning editor for science and natural history; while Harry Lansdown, former executive producer of factual independents, has been appointed commissioning editor for BBC3 features, formats and specialist factual.

The new appointments join the previously confirmed Martin Davidson as commissioning editor for history and business; and Jo Ball, commissioning editor for BBC1 and BBC2 features.

This commissioning team will report to Emma Swain, BBC head of knowledge commissioning, who was also appointed earlier this year.

George Entwistle, controller of BBC knowledge commissioning, said: "We now have a really strong team boasting some of the best talent and expertise in the business. Their vision, creative energy and knowledge of programme makers in the BBC and the independent community will enable them to commission the very best factual programmes. "

Jana Bennett, director of BBC Vision, added that the areas the jobs commission "go to the very heart of the BBC's public purposes".

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