The Government's NHS deep-clean programme, which officially finishes on Monday, is in danger of becoming an "expensive publicity stunt", a spokesman for cleaning firms said.
Unless long-term funding is secured, there is a good chance the situation will "slip back" to how it was before the programme started.
Other campaigners said some hospitals had carried out a "bit of a spring clean around the beds" and a "tick box" exercise rather than a deep clean.
Prime Minister Gordon Brown announced last September that every NHS hospital in England would be scrubbed in a bid to tackle bugs like MRSA and Clostridium difficile.
But the plan has come in for repeated criticism, including from contract cleaners, the NHS Confederation and opposition parties.
Andrew Large, director general of the Cleaning and Support Services Association, said many hospitals - "but not all" - will meet the deadline for completing cleaning.
About 40% of NHS cleaning services are out-sourced to private companies, which his association represents.
Health Secretary Alan Johnson announced on Saturday that 93% of NHS trusts would have their cleaning finished by the end of today.
But Mr Large said not all hospitals had been cleaned to the same standard and pointed to issues over funding.
Trusts have bid for different amounts of money from a central pot of £57.5m for the deep clean programme, he said.
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