The regulator's online register uses a red border to flag up charities that are late supplying their accounts (1 October, page 3).
An email sent by the commission to the Chernobyl Children's Project in response to a request by the charity for more time to file its accounts warned that late submissions would show on the charity's page for five years.
This could "have a negative effect on non-compliant charities, in particular if they rely on funding from the public or outside organisations", said the message, which was sent in July.
Linda Walker, national director of the project, said the letter was "draconian", given that the charity had outlined the reasons behind the delay.
A spokeswoman for the commission said she was unable to comment on a particular case. "We do not think that our approach to ensuring charities comply with their statutory duty to report is draconian," she said.
Most of the feedback the commission had received since the register's launch had been positive, she added.
- See Letters, page 12.