Under the regime, companies face a fine of 50% of the arrears that have built up as a result of the failure to pay the minimum wage with limits set between £100 and £5,000.
However, in some cases HMRC will consider prosecuting employers in the courts for which there is an unlimited fine.
Accountancy firm Moore Stephens said: "Where an employer has been in breach, the arrears are calculated at the rate applying when the breach is discovered, not the rate ruling at the time of the breach, which means that settlements will be more significant in future."