The regulator introduced a system on its website last week that highlights the organisations that have filed their accounts late with a red border (1 October, page 3).
Some charities that have seen their records on the online register bordered in red expressed their dismay at the new system.
Laurence Stein, development director at the British Friends of Boys Town Jerusalem, which raises money for a Jewish boys' school in Israel, said the new system was unfair and unjustified. "The commission should contact the charities first," he said.
Linda Walker, national coordinator at Chernobyl Children's Project (UK), which works with children affected by the 1986 nuclear disaster, said the charity had been given a red border even though this was the first time it had filed its accounts late.
"I think it's very unfortunate that we are being branded in this way," she said. "This is the first time it's happened and our accounts will be supplied shortly."
Walker said the delay occurred because the charity changed its treasurer and accountants; she had written to the commission explaining the circumstances in July, ahead of the deadline.
Derek Vitali, head of finance at Bowel Cancer UK, said he was disappointed at the culture of naming and shaming. He said, however, that the charity would have to "raise its game".
The charity said that its accounts information had already been sent to the regulator. However, a spokeswoman for the commission said the data had not been received.
Miriam O'Keeffe, project manager at the BBC Performing Arts Fund, said the charity had a scramble to file its documents after it became aware that its accounts were overdue and its record was highlighted in red.
The commission spokeswoman said charities were reminded their accounts were due as the deadline approached.
"The new register enables supporters to be better informed and also intends to make charities even more accountable to all their donors and beneficiaries," she said.
- Charities with annual incomes of more than £10,000 are required to submit financial documents
- The deadline for receipt of accounts and annual returns is 10 months after the end of a charity's financial year
- The register is the first step in the regulator's campaign to improve compliance rates
- Failure to supply the documents could lead to removal from the register, the commission has warned.