Primary care trusts are struggling to improve as quickly as other sectors and have seen a decline in the quality of their services.
PCTs emerged from the annual health check as the worst-performing trust type for the second year in a row, with reconfigured organisations doing particularly badly.
Their score for quality of services has dropped, with the number rated as excellent or good tumbling from 33 to 26 per cent and the number labelled weak growing from 8 to 12 per cent. Only two were rated excellent: Birmingham East and North, and South Tyneside.
However, PCTs have improved their 'use of resources' score this year, with 19 per cent rated good or excellent compared with 8 per cent in 2005-06.
The number rated weak has dropped from 41 per cent to 29 per cent. Barking and Dagenham PCT managed to jump two grades, from fair to excellent.
But PCTs still lag a long way behind the other sectors such as acute (49 per cent good or excellent) and mental health trusts (55 per cent good or excellent).
Ten PCTs were given a double weak rating, nine of which were reconfigured during the 2006-07 assessment year.
Nearly all - 96 per cent - of the 72 reconfigured trusts scored weak for use of resources. For quality of services, this was 88 per cent.
Anna Walker, chief executive of the Healthcare Commission, said even PCTs that had not been reconfigured 'still haven't done well'.
'PCTs have very demanding targets because they're about the health of the population.
'The targets on which they have done especially badly - convenience/choice, handling high-intensity users and practice-based registers - are all things that really matter to people.'
Ms Walker accepted that reconfigured trusts may be experiencing 'teething problems' but she expected them to have made significant progress by next year's health check.
Unsurprisingly, the area with the highest number of weak PCTs for quality of services was in the Healthcare Commission's central region, which also had the greatest proportion of reconfigurations.
However, the commission's annual health check report also questions why London PCTs did not get better results, given the city has not seen any reconfigurations.
More than a quarter of PCTs in London were weak on their use of resources, although only one trust got the bottom score for quality of services.
The report predicts 'a significant upturn in performance for reconfigured PCTs in 2007-08, as they will have had the chance to bed down and identify and address any areas of concern'.