The new Carbon Reduction Commitment requires business over a certain size to start measuring their energy use as the first step towards a new carbon trading scheme.
Once the scheme is up and running, from April 2011, those companies that cut the most carbon will be rewarded while those at the bottom of the league table will face financial penalties.
Around 5,000 companies are required to register for the new 'green tax' by 30th September or face fines of up to £45,000.
But new analysis by PricewaterhouseCooper said companies need to have completed the paper work by 2nd September in order to allow for checks by the end of the deadline.
The leading accountants also calculated the costs of the CRC are much higher than expected. Every company will have to spend around £20,000 in the first year on the costs of complying with the scheme such as paperwork and staff time.
The biggest companies will have to spend £500,000 over the next five years if they fail to cut carbon.
Henry Le Fleming, carbon reporting specialist at PwC, said companies have just over two weeks to register.