The department will send letters to businesses that it believes are at risk from poor bookkeeping, followed by a telephone call to discuss their records.
If it is decided that a visit from HMRC is required - and poor record keeping is found - businesses will be given help and guidance on how to improve.
A follow-up visit will then take place three months later. If improvements have not been made, HMRC may charge a penalty to the business.
HMRC's Director of Local Compliance, Richard Summersgill, said the scheme is designed to help enterprises with poor records.
"Adequate records help businesses pay the right amount of tax at the right time, thereby avoiding interest and penalties for errors and late payment, whilst also giving HMRC greater assurance when a business submits its tax returns," he explained.
The scheme will be launched over a 14-week period, with London and Anglia (November 26th), south-east England (January 14th 2013), Scotland (January 14th 2013) and Northern Ireland (January 14th 2013) the first areas to see it come into force.
Indeed, the programme will be in place everywhere by February 4th next year and small businesses could seek advice from a specialist accountancy firm in the meantime to ensure their records are accurate.
Posted by Thomas Fletcher