Locums who operate through a limited company face an additional financial penalty from a drop in the tax-free dividend allowance from £5,000 to £2,000, specialist medical accountants say.
Under changes unveiled by chancellor Philip Hammond on Wednesday, the main rate of national insurance contributions (NICs) for self-employed people will rise.
Class 2 NICs are paid on profits of £5,965 or more, and class 4 NICs on profits between £8060 and £43,000. From 2018, Class 2 NICs will be abolished, but Class 4 NICs will rise to 10% in April 2018 and to 11% in April 2019.
James Gransby, an executive board member of the Association of Specialist Medical Accountants (AISMA) and head of healthcare at MHA MacIntyre Hudson said: 'For GP partners already under financial pressure from high rates of tax and suffering from attacks on their pensions in recent years, the news that their main rate of class 4 national insurance contributions will rise by 2% over the next two years from 9% to 11% will be a bitter pill to swallow.
'Not least because this all but wipes out the promised income increases recently announced in the 2017/18 GP contract review.'
He added: 'For locums the fall in the tax free dividend allowance from £5,000 to £2,000 per year from April 2018 will be a blow for those operating through a limited company and follows hot on the heels of a 7.5% increase to dividend rates that they are already reeling from. The tax cost of this change for a husband and wife owning shares in a limited company who are both higher rate taxpayers will be £1,950 per year, and more for additional rate taxpayers.'
GPC deputy chair Dr Richard Vautrey hit out at the wider failure of the budget announcement to tackle 'the enormous pressures overwhelming general practice in England'.
'We are concerned about the possible implications of the national insurance changes on both GP partners and locums, and will be seeking further clarification from the government on how this will operate in practice,' he said.
A Treasury statement on the changes said: 'Taken together, only a self-employed person with profits over £16,250 will have to pay more as a result of these changes.
'This better reflects the fact that the differences in contributory benefit entitlement between the self-employed and employees are now small, following the introduction of the new state pension in April 2016.
'In the summer, the government will also consider whether there is a case for greater consistency in parental benefits between the employed and self-employed.'