Some GPs could be faced with tax bills as high as £30,000, according to Laurence Slavin, partner at medical accountants Ramsay Brown & Partners.
In October, the government announced the annual allowance for tax-privileged pension saving would be reduced from £255,000 to £50,000 per year from April.
The new rules apply to public and private pension scheme members and will hit those earning £100,000 or more.
In its written evidence from the UK health departments to the NHS Pay Review Body last month, the DoH admitted that 10,000 high-earning members of the NHS pensions scheme would be affected - 'primarily GPs, medical consultants and very senior managers'.
Mr Slavin estimated that 25% of principals would be hit.
Dr Andrew Dearden, BMA's pensions committee chairman, disagreed.
'It will affect a very small number of GPs. You'd need a number of factors coming into play to end up with a hefty tax bill,' he said.
These factors included high earnings, paying into the NHS pension scheme for over 20 years and buying added years.
Mr Slavin said: 'Any GP over 45 will have been paying into the scheme for more than 20 years. And, if you go into a practice, one or two partners are paying added years, so it's not that unusual.'