The average practice in England lost around £3,000 on the patient survey for 2008/9, GP newspaper can reveal.
The total loss to the profession in England is around £24 million, and UK-wide losses come to around £32 million.
But analysis of the results shows that two-thirds of low-scoring practices had response rates that were not statistically sound.
More than 65 per cent of practices that scored below average on the disputed advanced booking question, PE8, had response rates so low their results fell outside the DoH's statistical confidence limits.
Over 16 per cent of practices in England lost all 35 QOF points for PE8, worth £4,437 to an average-sized practice. Over 85 per cent of these practices had statistically unsound results.
Nearly 11 per cent of practices lost all 23.5 QOF points on the PE7 48-hour access question, worth £2,979 to an average-sized practice. Just under half of these practices' results were statistically sound.
In total, 2,657 practices' results fell outside the accepted statistical confidence limits for PE8 - nearly a third of the 8,266 practices in England.
Average scores were 84 per cent for PE7 and 76 per cent for PE8, which would earn an average-sized practice £4,499 out of a possible £7,416.
Health minister Mike O'Brien said the DoH would look at how to make the survey more sophisticated, but insisted its methodology was sound.
The losses were 'a relatively small penalty' for practices that had not performed, he said.
Overall, pollsters Ipsos Mori found that 'the majority of patients are overwhelmingly positive about their GP'.
Welsh practices lost an estimated £2 million in total and the same amount was lost in Northern Ireland. Scotland estimates its loss at £4 million.
GPC deputy chairman Dr Richard Vautrey said primary care organisations have yet to respond to the thousands of practices appealing against their results.
The 2009/10 patient survey has been sent out and is subtly different. It is being posted to waves of patients quarterly, instead of in one single mail-out.
Dr Vautrey warned that quarterly results may 'vary wildly'.
|Patient survey results|
15% of practices scored full marks (>90 per cent) for both QOF patient experience indicators, PE7 and PE8, worth £7,416 to an average practice
32% (2,657 practices) had response rates that fell outside the accepted statistical confidence limits - of these, 88 per cent scored below average
17% (1, 387 practices) achieved none of the 35 points for PE8 - 85.5% of these results fell outside confidence limits
10.6% (879 practices) achieved none of the 23.5 points for PE7 - 49 per cent of these practices' results fell outside confidence limits
3.3% (273 practices) scored no points for both PE7 and PE8.