The HMRC is offering a three-week 'amnesty' for doctors who may have underpaid tax in the past to rectify the situation.
From April 2010, the HMRC will investigate doctors they believe have not declared their full income, dating back up to 20 years.
Doctors who make a voluntary disclosure will be asked to pay the full tax they owe and a penalty of up to 10%.
Accountants and legal experts say the campaign, called the Tax Health Plan, will provide ‘easy pickings' for a treasury looking to raise every possible penny of tax revenues.
Jason Collins, a partner at the law firm McGrigors, said that although HMRC often targets its compliance work at specific sectors, ‘to do so in the form of a tax amnesty aimed solely at the medical profession is without precedent'.
GPC chairman Dr Laurence Buckman said the campaign would not be a problem for GPs who have kept thorough records.