However, the second annual check found that performance was improving, with 29 per cent of PCTs' use of resources scored as 'weak' compared with 41 per cent last year.
Overall in 2007, 3 per cent of PCTs were rated excellent (0 per cent in 2006), 16 per cent good (8 per cent) and 51 per cent fair (51 per cent).
The results were published at the same time as research from the Association of Directors of Public Health which showed that £95 million of funding set aside to tackle health issues such as obesity, alcohol abuse and sexual health was instead used to pay off PCT financial deficits.
Andy McKeon, managing director for health at the Audit Commission, which reviewed the finances of all non-foundation trusts for the Healthcare Commission, said: 'There has been an improvement overall. Some are on the road to recovery and some are at the other end of spectrum.'
Healthcare Commission chief executive Anna Walker said: 'Fair means adequate, and adequate is not good enough for a world-class system. The challenge is seeing more NHS trusts moving from fair to good.'
The 72 recently merged PCTs performed the least well. Re-organisation of resources was blamed for the poor performance but Healthcare Commission chairman Professor Sir Ian Kennedy hoped the merged trusts would benefit from economies of scale in the long term.
'This year we are setting a benchmark for these new PCTs for the future. We would expect them to move towards the better end of the graph,' he said.
South West and South East Coast SHAs were highlighted as the worst performing regions, while the North East and Midlands were praised.
Gary Needle, head of the annual review, said there was a 'hard core' of trusts with serious financial standing and management problems.
Seventy per cent of PCTs failed the target relating to convenience and choice, which says that patients should be able to choose from at least four providers paid for by the NHS.
This was the worst area of performance in any of the existing national targets. The reasons for this included GPs not being contractually obliged to offer choice and IT problems.