The commission aims to release a report on every statutory inquiry it opens, but has the power not to do so when it thinks that publication would have "a detrimental impact on the effective regulation of the sector and public trust and confidence in charities".
The regulator declined to tell Third Sector the names of the charities involved and was unable to confirm precisely how many reports had been suppressed.
A spokesman said the commission did not keep a centralised log of unpublished reports and was not in a position to go through every inquiry it had carried out in the past two years.
According to the commission's recently published report Charities Back on Track, which summarises the lessons from its recent compliance work, the regulator published 42 inquiry reports in 2007/08, opened 19 new formal inquiries and closed 29 (10 September, page 1).
Almost 75 per cent of inquiries were completed within the target period of nine months, but only 31 per cent of reports were published within three months of case closures, according to the report.