The health watchdog has been forced to apologise to hundreds of GPs for giving them incorrect patient safety risk ratings.
More than 7,000 GP practices in England were put into one of six risk bandings, which could trigger early inspections.
But a BBC investigation has found serious errors in the calculations used by the Care Quality Commission (CQC).
Around 60 practices have been taken out of the high-risk category and four low-risk surgeries need early inspection.
Practices were judged on 38 indicators of performance, ranging from how easily patients managed to get appointments to how good doctors were at picking up conditions such as dementia.
Practices were graded in six bands, with Band 1 being the highest concern, and Band 6 the least risky.
The majority were of low concern, but 11% were rated in the highest risk band.
Bad dataThe BBC discovered that for one indicator, whether patients were able to get an appointment with a GP or nurse the last time they tried, the calculations were so flawed that the CQC has been forced to remove the indicator altogether.
A further four indicators had to be refined based on revisions to data provided to the CQC by NHS England.
Hundreds of practices will now be assigned a different band.
In its initial register, published two weeks ago, the health watchdog ranked 7,276 practices out of the total 7,661 in England, and placed 864 practices in the "highest concern" category.
Original rankingsAs a result of the recalculations, around 60 practices will be lifted out of the "highest concern" category, and four that were previously deemed low-risk have been found to be in need of early inspection.
The CQC has not confirmed the total number of practices that will be rebanded in the review, but the BBC understands it will be around 350, or 5% of all GP surgeries.
The CQC register was set up to help target inspections, and the watchdog said it did not necessarily indicate poor GP surgery performance.
Sir Mike Richards, chief inspector of hospitals for the CQC, told the BBC: "We will make them a big apology. This only became apparent when we ran the data on the thousands of practices rather than just the hundreds that we tested them on."
He defended the publication of the risk bands in the interest of transparency.
He said: "We are using the data to help us know where we might go first. Our judgement comes from a combination of data and inspection. The main thing that is going to matter is that we are going to be inspecting every practice."
Poor dataMeasures removed
- Whether patients were able to get an appointment with a doctor or nurse last time they tried
Measures recalculated
- Coronary heart disease incidence
- Chronic obstructive pulmonary disease (COPD) incidence
- Unnecessary A&E admissions
- Dementia diagnosis rates
The British Medical Association said mistakes by the CQC risked "doing serious harm" to the reputation of good surgeries.
Its GP committee chair, Dr Chaand Nagpaul, said: "We warned at the time that simplistic targets would fail to take into account the enormous pressures GP practices are facing, and that skewed and limited information does not tell us about the quality of care.
"These failings have the potential to seriously undermine the trust in the system and patients' confidence in their GP and it is only right that all of those practices affected are now contacted and receive a full apology."
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