The letter urges congregations to report any suspicions they might have about other worshippers to the police.
"Islam categorically forbids violence and killing of innocents, let alone indulging in violence which can cause death and mayhem," it says.
"We therefore urge you to observe the utmost vigilance against any mischievous or criminal elements from infiltrating the community and provoking any unlawful activity."
The MCB's appeal to the UK's two million Muslims will be made through imams, chairmen and secretaries of mosques. Hundreds of thousands of booklets will also be sent out.
But Masoud Shadjareh, chairman of the Islamic Human Rights Commission, told Aljazeera.net that the letter's assumptions are false.
"As Muslims, we need to challenge stereotyping and injustices, rather than becoming party to them. I'm not questioning the MCB's intentions but it seems that they are reacting without thinking"
chairman, Islamic Human
"As Muslims, we need to challenge stereotyping and injustices, rather than becoming party to them," he said. "I'm not questioning the MCB's intentions but it seems that they are reacting without thinking.
"I know that they have been put under a lot of pressure but this sort of action is pointless, reactionary and actually creates the very Islamophobia that we are trying to fight. I can't put it more strongly than that."
Number of arrests
Iqbal Sacranie, the director of the Muslim Council of Britain, dismissed the charge as "utterly nonsensical".
"The only response some elements have to a positive and constructive initiative is to try to undermine it," he told Aljazeera.net. "How can this letter be Islamophobic?
"It is facing the reality that there are a large number of arrests taking place in the community. Although, by the grace of God, most are released without charge, some are convicted. One Muslim conviction is one too many."
In fact there have been two Muslim convictions for terrorism offences since the September 11 attacks. But there have also been more than 500 arrests and a dramatic shift in police "stop and search" policies.
Last year, police made 32,100 searches under the Terrorism Act, an increase of 30,000 on the figure for 2000. Community leaders say that the vast majority of those targeted have been young Muslims.
For Abd al-Bari Atwan, the influential editor of the al-Quds newspaper, the MCB's decision was not unexpected.
"The Muslim community in Britain is facing a critical time because the media have launched a hate campaign against them since the Madrid bombings," he told Aljazeera.net.
"Every Muslim is now a suspect and everyone is being watched by the police and intelligence services in one way or another."
The controversy over the MCB letter closely followed the arrest of eight British Muslims on Monday, for their part in an alleged al-Qaida bomb plot. On Wednesday a judge granted police a further three days to question the men. Police said that half a ton of ammonium nitrate, a fertiliser
The fertiliser was recovered from
a self-storage facility in London
that can be used to make explosives, was recovered during the operation.
Dr Sacranie denied that the MCB's letter was a panic response to subsequent media headlines such as the Daily Telegraph's "Islamic bomb attack foiled" which proved offensive to so many in the Muslim community.
"This initiative is part of our long-term action plan," he said. "We feel the pressure day in and day out to do something for the community and for the country."
"To talk about 'Islamic terrorism' is a contradiction in terms, as Islam is a religion of humanity that utterly and totally condemns acts of violence and terrorism. Yet we are the only community that is being linked with terrorists."
But he singled out extremist groups such as al-Muhajiroun, for targeting alienated Muslim youths.
"Within our community, there are elements who try to create hatred against people of other faiths," he said. "We are telling the youth we share their concerns about the atrocities being committed in Palestine but it is unacceptable to use violent means in the UK."
Shortly after the letter was released, the UK's National Union of Students moved to "no platform" or ban al-Muhajiroun, the Muslim Public Affairs Committee and Hizb al-Tahrir from speaking at any campus in the country.
The three groups have been associated with anti-Semitic propaganda. But Atwan said al-Muhajiroun were "a very small group and a tabloid creation," while Usama Saeed of the Muslim Association of Britain described them as "an empty drum, they make a lot of noise, but in reality there is nothing much happening there."
Saeed told Aljazeera.net that he did not know whether the MCB letter would have a positive effect on the press hysteria. "There has to be vigilance in the community," he said, "But we also have to have the same rights and responsibilities as everyone else."
"I have never seen any terrorists recruiting or organising in mosques. If someone told me to weed these people out, I wouldn't know where to start. What is needed is a debate about the root cause of terrorism, which is our country's foreign policy"
Muslim Association of Britain
"I have never seen any terrorists recruiting or organising in mosques. If someone told me to weed these people out, I wouldn't know where to start. What is needed is a debate about the root cause of terrorism, which is our country's foreign policy."
The row over the letter, he added, was being taken out of context by the press.
One story the British media did not report the week before the alleged al-Qaida bomb ring was smashed, was cited by many Muslim leaders as an example of the animus they are now facing.
A 17-year-old Muslim girl was kidnapped in Ilford, East London
by a Christian fundamentalist who slashed a crucifix into her upper arms and side and tried to force her to recite the holy trinity.
When she refused, he repeatedly told her that "Christianity is the right religion" and slashed her every time he did so.
However, the tabloids did at least turn their attention to Ilford the following week. It was the home town of one of the alleged al-Qaida bombers.