Nearly all hospitals are failing to meet hygiene and cleanliness standards set by the government to prevent superbug outbreaks, inspectors say today. Most of the breaches are not serious, but the Healthcare Commission warns that only consistent and comprehensive controls in all NHS trusts will ensure that infection rates for MRSA, Clostridium difficile and other hospital-acquired infections continue to fall.

"At nearly all trusts we have found gaps that need closing," said Anna Walker, the commission's chief executive. "It is important to be clear that at these trusts we are not talking about the most serious kind of breaches. But these are important warning signs to trust boards that there may be a weakness in their systems."

At three out of the 51 trusts (around a third of the total) where unannounced spot checks took place, inspectors found serious breaches of the government's hygiene code. Bromley Hospitals NHS trust, Ipswich Hospitals NHS trust and Ashford and St Peter's NHS trust were all issued with improvement notices which require urgent action to safeguard patients. More than half of all the trusts were failing to keep all areas clean and well-maintained. One in five trusts did not properly comply with the rules on decontamination of instruments and other equipment used with patients. One in eight did not have adequate isolation facilities for patients who have picked up infections, which is extremely important for preventing the spread between patients on wards.

However, the commission said it was encouraged by the positive steps many trusts had taken to remedy the breaches it had identified. Out of the 51 trusts, only five had a completely clean bill of health. These were Barking, Havering and Redbridge Hospitals NHS trust, Kingston Hospital NHS trust, Leeds Teaching Hospitals NHS trust, St George's Healthcare NHS trust and St Helen's and Knowsley Hospitals NHS trust.

Walker said that generally, trusts were paying close attention to infection prevention and control and their efforts appeared to be bringing rates down. But the commission wants to see compliance with the hygiene code all of the time and for every patient. "It is the consistent application of these systems that will ensure infection rates continue to drop. These issues are a top priority for the public. We make no apologies for demanding high standards. We have been asked by the government to help maintain the concentration on these issues and we intend to do just that."

The commission is warning trusts that they must comply before they can register with the new Care Quality Commission, which begins work next April and will be able to impose conditions on trusts and levy fines if they fail.

Health minister Ann Keen said any breach of the code was unacceptable and trusts must take immediate action.