‘Substantial’ improvements in quality of care resulted from the introduction of the framework, according to research led by Tim Doran of the University of Manchester.
But by 2006/7, the quality of some GP activities not funded through the QOF was lower than predicted before the scheme began.
The authors said although elements of the QOF had helped to mitigate this impact, features such as computer prompts during consultation may have distracted GPs from non-incentivised tasks.
They added it was vital to monitor non-incentivised activity to ensure quality is retained.
The GPC said incentives can have a significant effect on patient care and any detrimental impact was 'only by a small amount'.
In January, the GPC had moved to defend the QOF, introduced in 2004 with £1bn of NHS funding. It was criticised after a study claimed incentivised targets for BP management have had no impact on patient outcomes.
In the new study, published in the BMJ, researchers studied a wider range of 42 activities – 23 incentivised, 19 not – selected from 428 indicators of quality care in general practice.
The team included members of the University of Manchester’s Primary Care Research Group that work for NICE to develop and amend QOF indicators.
They compared projected and actual achievement rates for all 42 activities.
Achievement had increased in the years prior to 2004 due to quality initiatives that would later form the bedrock of QOF indicators. But improvements accelerated after the QOF was introduced.
In some areas in 2004/5, achievement of such initiatives increased by up to 38% above projections.
Although rate of improvement reached a plateau by 2006/7, it remained higher than predicted by pre-incentive trends.
There was no effect on rate of improvement of non-incentivised activities after the QOF began. By 2006/7, achievement rates had fallen below those predicted by trends.
Authors concluded: ‘These findings show some important limitations of financial incentive schemes in health care, and the importance of monitoring, as far as possible, activities that are not incentivised in addition to those that are when determining the effects of such schemes.'
GPC chairman Dr Laurence Buckman said: 'Where incentives are used, the positive impact on patient care can be significant. Where the impact has been detrimental it has only been by a small amount.
'Treating the sick will always be the core of GPs' day to day work, but it should be remembered that the QOF was brought in partly to move towards a greater focus on preventative healthcare.'
He added: 'It has already been shown to have done this with the improvement in diabetes care for example. We believe the true impact on public health, as well as on the NHS budget, will only really start to be seen over the long term.'