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 GP investigation also found that 25% 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 from April this year 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 last April, and will hit practices' QOF achievement pay this June.
The switch to true prevalence will benefit many practices achieving high prevalence targets. 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 senior partner at Imperial College Health Centre in London, welcomed an invitation from Westminster PCT for practices to bid for LESs to supplement 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 Nottingham City PCT has declined to offer additional support. The PCT said practices could pursue existing LESs to replace lost income. Dr Porter said it wanted to ‘show equity and transparency' by treating practices the same.
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.