The department says that firms will have time to bring their records up to standard following checks and penalties will only be applied as a last resort.
But the Telegraph reports that the Chartered Institute of Taxation believes HMRC may not have the powers it needs to impose the fines.
However, a spokesman for HMRC told the news provider: "Penalties will only be charged where customers are found to have deliberately destroyed records on the first visit, or where they have failed to improve their record keeping to an adequate standard by the time [a] follow-up visit takes place.
"So before a penalty is considered a customer will have been given time to bring records up to an adequate standard."
The department unveiled the redesigned Business Record Checks programme at the start of the month, saying small firms will need to clearly demonstrate their tax obligations.
Posted by Thomas Fletcher