Figures released by the NHS Information Centre show the average exception rate rose to 5.41 per cent in 2009/10, up from an all-time low of 4.87 per cent in the previous year.
The NHS Information Centre said the rise was due in part to new outcomes-based clinical indicators.
Exception reporting had fallen since 2006/7, when it reached 5.83 per cent.Last year, practice-level rates varied across clinical indicators from 0.05 per cent to 61.5 per cent.
Almost half of all practices in England recorded exception rates lower than 5 per cent, while rates climbed above 15 per cent in 148 practices.
Eight of 16 indicator domains had increased exception reporting in 2009/10 compared with the previous year. Four of these - in COPD, depression, diabetes and heart failure domains - had new or revised indicators in 2009/10.
The heart failure domain had the biggest change from 2008/9. Exception rates rose 9.2 per cent in a single year to 17.2 per cent. This was due principally to the introduction of the new HF 4 indicator, which had an exception rate of 37.8 per cent. NICE is working on redefining exception reporting. It follows concerns about indicators for which there are high achievement and high exceptions.
The NHS Information Centre report concluded: 'The increase is probably partly due to changes in the QOF, including the introduction of new clinical indicators, in 2009/10.'