Researchers compared the performance of practices since the QOF was introduced in 2004 in terms of points scored and achievement rates.
They found practices with fewer than 3,000 patients had greater variation in performance than larger practices.
Such practices made up 45.1 per cent of the bottom 5 per cent of QOF achievers, but also accounted for 46.7 per cent of the top 5 per cent.
The study's authors believe small practices are losing out because achievements above the maximum threshold are not rewarded.
'The payment system does not adequately recognise the achievements of high-performing practices, many of which are small,' the researchers said.
But Dr Peter Swinyard, chairman of the Family Doctor Association, opposed a move to 100 per cent thresholds.
'100 per cent is a silly threshold for anything,' he said. 'There are always some people you cannot get hold of.'
Dr Swinyard warned that increasing QOF thresholds could demotivate practices.