Of the 30 practices run by private providers during 2006/7, 16 achieved less than the average score for England of 954 points.
Across all practices run by private providers during 2006/7, the average score was 922, some 3 per cent below the English average, according to the NHS Information Centre.
Last month, GP reported that PCT-run practices averaged 810 points (GP, 30 November - PCT-run practices have 14% lower quality scores).
Among the lowest scoring practices run by companies were the Chilvers McCrea-run Brighton Homeless Healthcare Centre with a score of 752 and Intra Health's Chiltern Hills Medical Practice, Dunstable, Bedfordshire, on 800.
Other poor performers included Concordia's Parkside and Melbourne Grove medical practices, both in Southwark, south-east London, with 803 and 828 points respectively.
With the exception of one practice (Chilvers McCrea's St Luke's Medical Centre in Canning Town, east London), all 16 were also below the average scores for practices in their PCT areas.
Chilvers McCrea chairman Dr Rory McCrea explained that one reason why so many privately run practices under performed in the quality framework was 'because often they are practices that no one wanted to run in the first place and had a range of problems that needed fixing'.
The firm makes up the bulk of the list of the practices run privately during 2006/7 with 22.
'In some of our practices there have been historical problems with IT and HR. Some have been sorted quicker than others,' said Dr McCrea.
He added that he expected better scores from a number of his firm's practices with below-average scores in 2007/8.
Concordia Health, which is run by joint architects of the 2004 GMS contract Dr Simon Fradd and Dr John Chisholm, took over the Parkside and Melbourne Park practices in July 2006.
Dr Fradd said: 'We had a lot of catching up to do. Basics were not in place, such as no flu vaccines had been ordered.'
He denied that employing salaried GPs acted as a quality framework disincentive, an argument used to explain low scores in PCT-run practices.
'To be honest, you don't need GPs for the quality framework. It is not a GP function, most of it is administrative and nursing.'
Among the better performers were Care UK's Broad Street practice in Dagenham, Essex, with a score of 974. Also Intra Health's three other practices all had scores above the English average.
A spokesman for Intra Health added that the Chiltern Hills practice was expected to achieve a quality framework score of 950 by the end of the financial year.
GPC chairman Dr Laurence Buckman said: 'Many of these practices come from a low base to start with, so it is not a surprise that so many have low quality scores. What I would want to see is an improvement over time.'
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