UK defence officials have reportedly eliminated the Muslim Council of Britain's role in identifying and endorsing military chaplains.
The MCB had a voice within the Ministry of Defence's system for appointing chaplains despite a ban on the organisation working with the UK government.
Under the new orders sent out by ministers this week, the ministry must end the groups' involvement in endorsing imams to become military chaplains.
The MCB posted on its website on July 26 about the first Royal Air Force imam “endorsed by the MCB”.
The Telegraph newspaper first revealed the crackdown and said senior Conservative party officials had described the arrangement as “shocking”.
An defence spokesman said: “The UK government has a long-standing policy of not engaging with the Muslim Council of Britain (MCB), which is unchanged.
“The MoD complies with this policy. However, some contact with the MCB has been identified which we immediately stopped and we are investigating.”
Last year, Downing Street stated that ministers should continue to boycott the MCB. Gordon Brown’s Labour government in 2009 first set up the ban after the MCB's deputy secretary general Daud Abdullah signed the Istanbul Declaration, which called for violence against Israel and condoned attacks on British forces.
A report by Sir John Jenkins, the former UK ambassador to Saudi Arabia, in 2015 set out the history behind the decision to cut contact with the MCB, which he said seeks to exert influence over policy by cultivating politicians and officials.
It laid out how the Muslim Brotherhood shaped the Islamic Society of Britain, which went on to dominate the Muslim Association of Britain and played an important role in establishing and then running the MCB.
“In 2009, the then government suspended dialogue with the MCB after an office holder signed a public document which appeared to condone violence against any country supporting an arms blockade against Gaza,” the report said.
Sir John added: “There has been no substantive dialogue since then between any part of the [Muslim] Brotherhood in the UK and government.”
On Saturday, an MCB spokesman said the group's involvement with the ministry did not amount to nominating military chaplains.
“We will always support British Muslims taking part in our armed forces,” he said.