Over 28,000 medical professionals received warning letters from HMRC, and tax experts say investigations into practices could go on for years without GPs’ knowledge.
Just 1,500 medical professionals came forward to declare underpaid tax as part of this summer’s amnesty.
Paul Malin, director of tax investigations at BTG Tax, said HMRC could spend years dealing with all the cases because of a shortage of tax inspectors.
Even those who have come forward may still be investigated if they have different irregularities they have not disclosed, said Mr Malin.
The amnesty ended in June but HMRC is still advising GPs who think they may have underpaid tax to declare it as soon as possible.