The charity, which cannot be named for legal reasons, is in talks with the commission to have the information withheld, but may resort to legal action if this fails.
It this happens, it would be the first time a charity has attempted to secure an injunction on a freedom of information request.
The Freedom of Information Act does not apply to charities, but it does cover public bodies and the information they hold, so third parties can approach the commission to try to obtain information about charities. Only information that is protected by the Data Protection Act (such as trustees' personal details) is exempt.
A spokeswoman for the commission said: "We deal with any request for information under the act on a case-by-case basis.
"If a request was made for information that a charity had marked as being confidential, we could apply the 'public interest test', which involves determining whether it is in the public interest to disclose the information, or seek permission to release from those who provided the information to us, as required by the act."
According the Ministry of Justice, the Charity Commission received 84 requests for information under the act in the first three months of 2007.
Ben James, a solicitor at central London law firm Bircham Dyson Bell, said charities should be aware that information they send to the commission could be subject to publication, and should put in place Freedom of Information Act policies.
"Charities sometimes send more information than is required: for instance, they might send all their meeting minutes rather than extracts, and they might contain highly sensitive information," he told Third Sector. His recommendation is simple: if you aren't required to send it, don't send it.
The Freedom of Information Act 2000 gives people the right to access any information held by public bodies unless the latter can prove there are valid reasons for withholding it.
Voluntary organisations are not covered by the act unless they deliver services for public sector organisations.
Government departments and local authorities are covered by the act.