At the regulator's first open AGM last week, director of legal services Kenneth Dibble admitted that statutory inquiries into alleged malpractice at charities were often not effective. "They take far too long and accomplish too little," he said.
Under so-called Section 8 inquiries, the commission has the power to suspend trustees and employees, freeze bank accounts and stop fundraising.
There were 341 investigations opened last year, up from 258 in 2003/4.
Dibble added that the commission's policy of leaving inquiry reports on its website for two years could change too. "It can do great damage to a charity that has been put on a proper footing if, for example, it wants to attract funding," he said.
The commission also revealed that it was setting up a specialist unit to enhance its relationships with the UK's top 200 charities.
The Charity Engagement Unit will informally test new regulatory approaches such as impact reporting, provide assurance that the leading charities are well-governed and run, and supply evidence for regulatory reports, said Rosie Chapman, director of policy at the commission.
"The largest charities have the most complex operations, and they have quite an impact on how charities as a brand are regarded," she said. "We want to influence and to be influenced by the leading opinion-formers."
A director will be sought for the unit on a salary of £40,000. The five-person unit will begin operating by the end of the year.
Andrew Hind, chief executive of the commision, said the regulator was facing a real-terms cut in its budget from the Government, which has been frozen at £31m a year until 2008. "Money is tight and we are struggling to do all the things we want to do," he said.