The Muslim group, which claims to represent moderate Muslims in the UK, launched the attack on the BBC ahead of a 'Panorama' documentary to air next weekend, which details extremist roots of groups linked to the MCB.
In a letter to BBC director-general Mark Thompson, the MCB media spokesman, Inayat Bunglawala, claimed that the BBC was is more interested in furthering a pro-Israeli agenda than assessing the work of Muslim organisations in the UK.
"It is quite regrettable that at a time when it is of utmost importance that trust is built between Muslim communities across the country and the wider society, that the 'Panorama' team seem intent on creating mistrust by serving the interests of the pro-Israeli lobby and undermining community relations in the UK," Bunglawala wrote.
He added that the BBC should not allow itself to be used by what the called "the highly placed supporters of Israel in the British media" to make political capital out of the July 7 atrocities in London.
A BBC spokesman said: "The BBC rejects any allegation of institutional or programme bias and is confident that the 'Panorama' programme will be fair and impartial and a timely contribution to the present debate."
The BBC said it would respond to the MCB's allegations.
The news will come as a surprise to the pro-Israeli lobby, which has long accused the BBC of pro-Arab and pro-Palestinian views in its coverage of the Middle East.
The BBC 'Panorama' programme is a major blow to the MCB, which has had a high-profile role since the London bombings. Its secretary general, Sir Iqbal Sacranie, was knighted in the Queen's Birthday honours list in June and it has more than 400 groups linked to it.
Some of the affiliated groups are said to be involved in the extremist politics of Pakistan and it is these that 'Panorama' reporter John Ware investigates in the programme, in particular, the links with Jamaat-e-Islami, Pakistan's leading mainstream Islamist party.
A report in The Observer described this group as "an extremist sect". Sacranie has defended the group and said it was not involved with extremist politics.
In the programme, Ware also challenges Sacranie over his failure to attend the Holocaust Memorial Day and his attendance of a memorial service for Sheikh Ahmed Yassin, who was the leader of the Palestinian terror group Hamas.
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