An administrative blunder has stripped thousands of pounds from payments to practices across the UK in the last month.
All practices that rely on MPIG have had their correction factors inexplicably cut in statements for October, said the GPC.
Laurence Slavin, from specialist medical accountants Ramsay Brown and Partners, said GPs had contacted him to query income cuts that would amount to between £5,000 and £20,000 over a full year. Mr Slavin said correction factors had been cut by an 'unfathomable' amount with no explanation.
For a practice of average size the blunder will have cut around £1,750 from their core pay this month.
The DoH has confirmed it is investigating incorrect payments, but confusion remains over precisely how many practices have been affected.
GPC chairman Dr Laurence Buckman said it would affect all practices on MPIG. But one PCT told GP that only practices in areas that received supplements for high living costs had been affected.
Mr Slavin said he had seen examples mostly in deprived wards in Barnet and Brent, in north London.
A spokeswoman for Barnet PCT said: 'A number of GPs received incorrect payment from the PCT last month, as have practices in other areas.
'Barnet PCT is currently in the process of rectifying the situation, to ensure that all GPs who have been affected receive adjustments to their payments as soon as possible.'
A DoH spokesman said: 'We are aware that there have been some reported concerns that the Exeter payments system is not calculating global sum payments correctly, following the Statement of Financial Entitlement changes which came into effect at the start of October.
'We are currently investigating this issue to ensure that correct payments are being made in line with the new statement of financial entitlement.'
GPC chairman Dr Laurence Buckman said the GPC and LMC leaders were aware of the problem but it was possible that many practices had not noticed the error on their statements.
He urged practices to contact their LMC if they suspected they had been underpaid.
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