The GPC made a 'strong case' to NHS Employers that the 1.74 per cent enhanced services uplift should apply only to directed enhanced services (DESs).
It argued that this would guarantee the new funding would reach the profession.
But NHS Employers accepted the government's demands that any uplift be applied equally across both DESs and LESs.
GPC negotiator Dr Chaand Nagpaul said this would make it impossible to ensure that all practices benefited equally from the funding uplift.
'The uptake of DESs is pretty universal, but the provision of LESs varies considerably between PCTs,' he said.
The situation is further complicated by the fact that many LESs are offered on a one-year basis, or change from year to year. As a result, the pay rise will vary 'in a postcode fashion'.
The lack of data on variations in LES take-up makes it difficult to estimate how much funding is at stake, however.
Separately, Dr Nagpaul said that the GPC was in 'active negotiations' with the DoH about the £50 million in funding lost because of the late arrival of last year's clinical DESs.
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