The regulator says charities that submit their accounts late are unlikely to be well-managed, efficient and worthy of support, and has set up a searchable database on its website to allow local authorities to check up on charities.
But charities have criticised the commission, saying the idea that they are undeserving of licences if they submit their accounts late is too simplistic.
"If the commission really thinks that this will improve the standard of fundraising, sector transparency and public perceptions, they are on a different planet," said Martin Gomez, national co-ordinator at the Caring Cancer Trust. "A charity is not unworthy because its accounts are a few days late.
It is what is in the accounts that is important, and unless the information is clear and accessible instead of being written in accountants' jargon, the charity is not transparent because the public can't understand the accounts anyway."
Belinda McKenzie, administrator at campaigning group the Association for Charities, added: "This seems to be part of the Commission's organised war against smaller charities. Although it is important, submitting accounts on time is not charities' main purpose. If you are living hand to mouth and don't have the resources, it may be difficult. Smaller charities need help and support, not penalties."
The commission says that 31 per cent of charities are still breaking the law by submitting their accounts late. Simon Gillespie, director of operations at the commission, said: "The public has every right to know how charities spend their money."