Payments in 2004/5 and 2005/6 were based on estimates, but final figures released this year show some GPs were overpaid. Primary care organisations (PCOs) are now clawing money back from practices, which are liable whether or not the partners who benefited have now left.
Stuart Williamson, a partner at accountancy firm Williamson West said practices in England may have to repay up to £4,000 a year for the top earning GPs.
He said that practices where partners have retired recently are particularly vulnerable and could 'face an uphill struggle' recouping the money.
'I know of one practice that has lost more than £8,000 and another where a partner has emigrated and the practice has to pay back £2,424 on her behalf.
'It could be enormously difficult for practices to get the money back, especially if a partner has since died,' he said.
At least one PCT has offered a partial reprieve. Gloucestershire LMC secretary Mike Forster said NHS Gloucestershire had agreed not to 'ask practices to pursue the estates of dead partners'.
But he added that 'in the case of partners who have moved to other practices or ceased to be partners there may be negotiation to be done'.
GPC deputy chairman Dr Richard Vautrey hoped other PCOs would copy Gloucestershire's approach. 'Clearly it is difficult for practices in some circumstances, especially if a partner has died.'
He said the GPC had been warning practices that they could be asked to repay seniority funding.
The final seniority factors for the two tax years from 2004 to 2006, which vary across the UK, were revealed in July.
In England, the final 2004/5 figure was £81,123, compared with an interim £75,000. The 2005/6 factor was £91,123, and the interim £80,940.
Mr Williamson explained that if a GP's income minus any seniority payments falls below two-thirds of the final seniority factor, then the practice will be liable to a 40 per cent clawback - which could be up to £4,000. Two-thirds of the 2004/5 payment is £54,082, and for 2005/6 this works out at £60,749.
Mr Williamson warned practices to prepare for possible over-estimates in future years, adding that final seniority factors had not yet been calculated beyond 2005/6.
- Practices may have to repay up to £4,000 per partner per year.
- Practices are liable even if the partner has left, emigrated or died.