The practices signed up to a local enhanced service (LES) for £5,000 but will now only receive £4,000 under the new national enhanced service for Wales agreed for 2007/8.
Practices with fewer than 3,500 patients are to be penalised. GPC Wales has protested but the Welsh Assembly is going ahead regardless.
Dr John Thompson, Caernarvon GP and Welsh representative of the Family Doctor Association, said: 'This is discriminatory. In small practices our overheads are higher and pro rata we pay more.'
Now Welsh LMCs have asked their local health boards (LHBs) to make up the difference to the practices that have lost out.
Neath Port Talbot is the only LHB that has so far agreed to make it up to small practices.
Head of primary care Debra Davies said seven practices would receive extra £1,000 payments.
A Vale of Glamorgan spokesman said it had not decided to make up the shortfall to the two affected practices.
Under the banded access enhanced service, practices with more than 7,000 patients will receive £6,000.
GPC Wales negotiator Dr Ian Millington said there are surplus funds from enhanced services in 2006/7.
It is understood that the requirements for practices under the new enhanced service will be similar to the LES, and centred around the drawing up and implementing of an access plan.
To qualify for the money this annual plan needs to highlight improvements made since last year's plan was introduced.
In addition, in Wales, each practice must ensure a member of the primary care team is available within 24 hours and patients can pre-book an appointment two weeks in advance.
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