It found that PCT-run practices in England achieved an average quality score of only 810 points in 2006/7.
They are under-achieving the average score for practices in England by 144 points or 14 per cent.
The poor results cannot simply be blamed on the location of the practices. Of the 76 PCT-run practices identified in 30 PCTs, 65 had quality scores below the national average while 67 had scores below their own PCT average.
The eight practices run by Bradford and Airedale PCT averaged 750 points - almost 190 points below the PCT average.
In Bolton, the seven practices run by the local PCT averaged total quality framework scores of 800, 115 points less than the PCT average.
The lowest scoring PCT-run practice identified by GP was the Meadowell Centre in Watford, run by West Hertfordshire PCT. Meadowell achieved a quality framework score of only 403, 560 points below its own PCT average.
A West Hertfordshire PCT spokeswoman said: 'It has a small, very specialised caseload which does not emulate the normal GMS/PMS practice profile for West Hertfordshire PCT.
'The quality framework achievement, on its own, is not representative of the specialised care that this practice provides to the registered patients.'
In Brent, north-west London, quality framework scores at PCT-run practices ranged from 580 to 920.
Jo Ohlson, director of primary care and community commissioning for Brent PCT, said 'The PCT has run salaried practices where a GMS practice has been struggling and there is some ground to be made up on chronic disease management.'
Rylla Baker, associate director of primary care commissioning at Lewisham PCT in south-east London, said that because PCT-employed staff were not paid on the basis of delivering quality scores, they were less likely to exception-report patients.
She added: 'I do not believe that the quality framework gives the full picture. The Gellatly Road practice (756 points) has improved year on year and we believe this is the most important factor.'
GPC deputy chairman Dr Richard Vautrey said: 'It is common knowledge that PCT-run practices have been struggling.
'They have higher running costs than GMS practices. The results show practices run by PCTs are failing.'
GMS and PMS practices offer better value for money as well as providing higher quality services, said Dr Vautrey.