Missing the Sept 30 deadline will mean an immediate £5,000 fine, and £500 for each day after that, up to a maximum of £45,000.
Another 15,000 smaller organisations are also required to register and could be expected to buy permits in the future. If they miss the September deadline, they face fines of £500.
WSP Environment & Energy, a consultancy firm, estimated that a total of 7,500 businesses would miss the deadline.
Greg Barker, the energy and climate change minister, who is overseeing the scheme said yesterday: “I understand the original complexity of the scheme may have deterred some organisations and I want to hear suggestions as to how we can make the scheme simpler in the future.”
Executives and business groups said that the scheme had been poorly communicated and publicised, leaving many companies in the dark.
One recent survey suggested that 53 per cent of executives had not even heard of the CRC and did not know whether their firm was affected.
The Environment Agency, which will run the scheme for the Government, has refused even to publish a list of the companies that are required to register.
The Coalition is pressing ahead with the CRC despite Conservative pledges to cut red-tape on businesses.
Business groups said the paperwork and costs involved in complying with the CRC scheme could put a significant new burden on companies already struggling in an uncertain economic climate. The Bank of England is expected to underline fears about the economy today with forecasts for faltering economic growth and persistent inflation.