Last month, the regulator announced it would start naming all charities into which they open inquiries, unless there were good reasons not to do so.
The move was met with a degree of scepticism, with some, including the MCF, worried about potential reputational damage to charities, especially if they were exonerated after investigation – although the forum also said it welcomed "more accountability and transparency in the sector".
In a letter to The Times newspaper, published yesterday, Hany El-Banna, chair of the forum, said Muslim charities were "very concerned about the change of policy".
He wrote: "We call for the immediate repeal of this policy. This could damage the reputation of charities that have not committed any wrongdoing, bringing their activities under intense media scrutiny and creating public uncertainty before due process. We are also concerned that disclosing an investigation may damage relationships with donors and partners critical to our work for our beneficiaries in the UK and around the world."
El-Banna again reiterated that the forum welcomed "the Charity Commission’s commitment to transparency and rigorous monitoring".
A spokesman for the forum said that the charity’s change of attitude since the policy announcement came after discussions with Sir Stephen Bubb, head of the charity leaders group Acevo. Bubb, who also met the chief executives of Islamic Relief and Muslim Aid, said in a blog post that there was a perception that the commission was "targeting Muslim charities in a disproportionate way", a suggestion the commission rejected.
The spokesman said the issue did not affect only Muslim charities and that repealing the policy would be "in the best interests of the sector as a whole".
A spokeswoman for the commission said: "Our move to make inquiries public as a matter of course came in response to increased public interest in information about charities under investigation, and in a move to increase transparency. Our view is that it is in the public interest to make inquiries public, unless there are special circumstances – for example, where an announcement might prejudice a police investigation.
"We are clear that the opening of an inquiry is not in itself a finding of wrongdoing, but an exercise to examine serious concerns in detail."
The spokeswoman said that the number of charities subject to inquiry was "a tiny proportion of the thousands on the register".