Practices could face five-figure bills when PCTs claw back four years' worth of miscalculated seniority pay, accountants have warned.
GPs' seniority payments are based on their length of service in the NHS and their earnings relative to the national average.
However, although GPs are required to submit superannuation certificates the winter after each financial year, the DoH has yet to release details of the average profits GPs made in any year since 2004/5.
PCTs are thus forced to make assumptions about average GP incomes when calculating seniority pay. If they wrongly believe a GP to be earning more than two-thirds of the national average, they will pay them full seniority pay, although they are entitled to only 60 per cent.
This means that highly experienced GPs, entitled to more than £12,000 in seniority pay, could have been overpaid by as much as £4,800 a year. If the mistake has been repeated over four years, they could now owe the PCT £19,200.
'That's a lot of money to ask a partner to repay,' said Laurence Slavin, an accountant with Ramsey Brown and Partners. Asked how many GPs were affected, he said: 'We don't know. But more than people think.'
Stuart Williamson, an accountant with Williamson West, said GPs who had recently gone part-time and seen their income fall were particularly at risk.
Where there are doubts over a GP's entitlements, practices should 'withhold that money until we get some clarity about the situation', he said.
A DoH spokeswoman said details of average income were still being calculated and would appear 'in due course'.
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