One in four PCTs froze PMS pay in 2009/10 despite DoH advice to award uplifts, a GP investigation has revealed.
Responses from PCTs show that others allowed uplifts only for practices with low income per weighted patient, or applied uplifts below the level recommended by the DoH.
In April, DoH director of primary care Ben Dyson wrote to PCTs advising them to raise PMS core funding by at least 0.7 per cent, in line with the minimum amount GMS practices received in 2009/10.
GP asked all PCTs what uplift PMS practices actually received. Of the 30 to respond, seven (23 per cent) admitted freezing PMS pay.
Others said they had only allowed uplifts to practices that earned less than £63.21 per weighted patient. The DoH letter pointed out that practices in this category should receive a pay rise of 'no more than 0.7 per cent' - in line with the rise for GMS practices.
However, a handful of PCTs gave higher rises to practices with low income per weighted patient to bring them in line with better-off practices.
More than 42 per cent of GP partners now work under PMS contracts. National Association of Primary Care president Dr James Kingsland, who helped develop the contracts, said PCTs were 'raiding budgets' without considering why PMS practices receive more funding than their GMS counterparts.
'It shows a lack of understanding of what PMS is and why there are differences in contract values,' he said.
Under the DoH's World Class Commissioning framework, PCTs must demonstrate value for money in primary care contracts. But Dr Kingsland said: 'It's hardly world class is it, to just say one type of contract will not receive the uplift this year.
'What PCTs will get in return is challenge, confrontation and stagnation, and increased inefficiency.'
David Stout, director of the NHS Confederation's PCT Network, said the guidance was not obligatory and PCTs 'have the freedom not to follow it'.
'It entirely depends on the PCT's view on whether the practices are delivering value for money,' he said.
'It is about negotiation locally. You could say GMS practices are just as prone to money- saving cuts nationally.'
Last month, a document by DoH advisory body Primary Care Commissioning instruc-ted PCTs to cut money from PMS baselines, squeeze more work into current contracts and not to award DDRB uplifts.
PMS practices across England have also faced aggressive contract reviews over the past two years, with GPs in Suffolk fighting off cuts of up to a third of their income.
Laurence Slavin, from specialist medical accountants Ramsay Brown and Partners, said: 'PCTs are trying to level out earnings, with the really low-earning practices receiving an uplift, and unfortunately the higher-earning practices having baselines cut.'
A DoH spokesman said PCTs have the final financial responsibility for PMS contracts. The decision not to uplift a practice's pay may help reduce inequalities across the PCT, said the spokesman.