Less than a quarter of primary care trusts believe their services have met all government quality standards.
Only 23 per cent of PCTs say they complied with all the core standards in the annual health check during 2007-08, down from 31 per cent the year before.
This is the second successive year that PCTs have shown a drop in full compliance.
The 8 per cent fall compares with a 10.5 per cent increase in mental health trusts, 2 per cent rise in acute trusts and 5 per cent drop in the ambulance sector.
And 57 out of 152 PCTs admitted failing on parts of the hygiene code, the highest proportion of any sector.
Healthcare Commission head of assessment and methods Gary Needle said: "PCTs were the poorest performers. They're still relatively new organisations but boards have been in place for over a year now."
NHS Confederation primary care network director David Stout said he was pleased to see a 9 per cent improvement in the number of PCTs achieving 90 per cent compliance but there was still some way to go.
"More than 10 of the most improved trusts are PCTs. When we look at where PCTs are failing on the hygiene code, the standard they're doing less well on is about decontaminating reusable medical devices."
The overall compliance rate was 96 per cent, up from 94 per cent in 2006-07. The best performing sector, apart from the two learning disability trusts included in the assessment, was mental health, where 60 per cent hit all core standards.
They were followed by 47 per cent of acute trusts and 36 per cent of ambulance trusts.
There were big regional variations, with nearly two-thirds of trusts in the North declaring full compliance, compared with just over a fifth in the South West.
Foundation trusts were improving slightly faster than the rest of the NHS but 25 failed to meet all standards.
The standards trusts struggled most with were decontamination, equality, patients' records, training and using medical devices safely.
There were also improvements in the number of trusts that claimed to be reducing the risks of healthcare-acquired infections, supporting patient dignity and learning from incidents.
The Healthcare Commission will now carry out risk-based and random inspections to check the accuracy of trusts' statements, before the final results are published by the new Care Quality Commission in October.