Data from 103 PCTs suggest that although a minority of practices face large swings in QOF pay, most will see their pay rise by a small percentage.
The investigation also found 25 per cent of PCTs in England have still not assessed how prevalence changes in 2009/10 and 2010/11 affect practices.
GP leaders said it was 'theoretically possible' that practices could have up-front aspiration pay for QOF work clawed back by PCTs that had failed to account for the change.
Changes that took effect this month mean practices with low disease rates no longer have their prevalence 'rounded up' to boost their pay.
The square root adjustment, applied to limit the impact of prevalence weighting on QOF pay, was removed in April 2009, and will hit practices' QOF achievement pay this June.
The switch to true prevalence will benefit practices with high levels of disease. In Newcastle, the biggest 'winner' is predicted to gain about £70,000 per year.
But other practices will suffer drops in income, with university practices with low prevalence likely to be hit hardest.
One university practice is set to lose around £119,000 from QOF pay for 2010/11, after a loss of £88,000 the year before.
Support from PCTs to help practices affected by the changes has also varied.
Dr Irene Weinreb, a partner at Imperial College Health Centre in London, backed NHS Westminster's plans to offer practices local enhanced services (LESs) to boost their income.
Dr Hugh Porter, a GP at the Cripps Health Centre at Nottingham University, said prevalence changes posed 'significant challenges' to the practice.
But NHS Nottingham City has declined to offer additional support. The PCT said practices could pursue existing LESs to replace lost income. Dr Porter said the PCT wanted to 'show equity and transparency' by treating practices the same.
Dr Weinreb said it was 'short-sighted' of PCTs not to offer special support for university practices, which face challenges such as sexual and mental health issues. 'It's a ridiculous attitude. PCTs need to be more flexible.'
Support from PCTs was 'a postcode lottery, not just for patients but for practices too', Dr Weinreb said.
GPC chairman Dr Laurence Buckman said it was 'disappointing' that PCTs had failed to heed advice from the GPC, DoH and NHS Employers to prepare for QOF changes.
'This is not about money, but making sure resources are available. PCOs need to know which practices are at risk.'
Several PCTs planned to wait for 2009/10 QOF data later this year to assess the impact in 2010/11. Others appeared confused. NHS West Essex said it was 'not aware of any changes to prevalence in 2010/11'.
A DoH spokesman insisted: 'PCTs should have been working with their practices throughout 2009/10 to prepare for this change.'
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