All NHS trusts were asked to say whether they met 44 key standards in a new high-trust ratings system devised by the Healthcare Commission to replace star ratings.
The two most common standards PCTs failed to meet were having a systematic approach to maintaining patient records and ensuring healthcare staff undertook mandatory training.
About one PCT in four did not meet, or could not prove it had met, the patient record target. One PCT in five failed to meet, or could not prove it had met the training target.
Swale Teaching PCT, in Kent, admitted not meeting 25 out of 44 standards it was expected to achieve, the worst result in England.
Across all 570 primary and secondary care NHS trusts in England, about 18 per cent could not give an assurance that they had a systematic approach to keeping patient records.
Healthcare Commission chief executive Anna Walker said: 'We are encouraged by the way many boards have put their hands up and declared non-compliance with some of the standards.'
GPC negotiator Dr Andrew Dearden said the DoH had set so many targets that it was difficult to draw any conclusions from the results.