HM Revenue and Customs (HMRC) launched a 'tax health plan' this year, offering greatly reduced fines for medical professionals who voluntarily declared unpaid tax.
Just 1,500 of 30,000 doctors identified by HMRC as potentially having unpaid tax came forward by the 1 August amnesty deadline. These doctors paid only a 10 per cent fine on top of any tax owed.
HMRC has confirmed full investigations will now begin. Doctors found to have unpaid tax could face a maximum penalty of 100 per cent of the tax owed, on top of full repayment of the debt, plus interest.
An HMRC spokeswoman said the tax office was pleased its campaign had recovered 'millions of pounds of tax that might otherwise have been lost'.
She added: 'Anyone who has been evading tax should talk to us as a matter of urgency as voluntary disclosure always makes financial sense.
'Although we are starting on 1 August, it will take a few months to get through all of the potential cases, so anyone who has not come forward should do so quickly.'
Gary Ashford, chairman of the Chartered Institute of Taxation's management of taxes committee, said he was surprised by the low number of doctors who came forward.
'If only 1,500 have come forward, that is a considerable surprise and suggests that either many professionals are not taking this seriously, or of course that HMRC has failed to get its message across properly,' he said.
'Any medical professional with undisclosed tax liabilities really should take advice and start getting their affairs in order. It's clear to us that HMRC is intending to come down hard on defaulters.'