Only one in 10 hospitals is fully compliant with the government's hygiene code, a Healthcare Commission review suggests.
Of 51 trusts visited unannounced by the regulator, only five met all the requirements.
Only a handful of the breaches represented an immediate risk to the safety of patients, however.
Improvement notices were served to Bromley Hospitals, Ipswich Hospital and Ashford and St Peter's Hospitals trusts.
Overall, the commission report praised trusts for showing increasing commitment to reducing healthcare-associated infections.
Most had improved leadership, put in place policies on uniforms and appointed staff with responsibility for infections.
However, 27 trusts were failing to keep all areas clean and well maintained. One in five trusts did not comply with all decontamination requirements, and one in eight had inadequate isolation facilities.
Commission chief executive Anna Walker said: "Trusts have made real progress, with many getting good systems in place and demonstrating clear board leadership on this important issue.
"Where we have raised concerns, we have generally been encouraged by the positive and prompt response at those trusts.
"Now the challenge for trusts is to ensure they drive further sustained improvements by getting the right systems in place all of the time. At nearly all trusts we have found gaps that need closing."
Read the report at www.healthcarecommission.org.uk