Average achievement fell from 969.1 to 960.8 points between 2011/12 and 2012/13, according to latest figures released on Tuesday by the NHS Health and Social Care Information Centre.
It represents a 0.8 percentage point fall in average practice achievement, the first fall in three years.
The figure equates to drop of around £9.6m across England, worth nearly £1,200 per practice.
But the percentage of practices achieving maximum points leapt from 2.4% to 3.7% in this period.
More practices failed to achieve 90% of points or greater, rising from 6.3% to 9%.
Nationally, exception reporting rates fell by 1.5 percentage points to 4.1%.
The largest rise in QOF achievement was in the organisational domain, which rose by 0.9 percentage points.
Practices saw a fall of 4.6 percentage points in smoking indicators in 2012/13, the largest drop among clinical domain targets, while points earned in the dementia indicators fell by 1.8 percentage points.
Achievement of the other clinical targets was broadly the same as the previous year. The largest rise, of 1.2%, was seen in the depression targets.
Meanwhile, the number of patients on registers for the primary prevention of cardiovascular disease rose by 32% to 1.2m, while the number of registered patients with dementia rose by 8.5% to 319,000.