NHS hospitals are likely to miss targets to complete deep cleaning operations by the end of March.
Prime minister Gordon Brown previously announced a £60 million programme to improve hygiene at public health centres in order to remove the threat of super bugs such as MRSA.
Currently, ministers expect 93 per cent of hospitals to finish cleaning operations before the deadline while others are in the process of being disinfected.
Information obtained by the Conservatives under the Freedom of Information Act also indicates that problems had occurred in providing funding for the programme. The Tories claim that only 25 per cent of the funds earmarked for the programme had been transferred to the NHS.
Shadow health secretary Andrew Lansley has called the programme a "shambles", adding that NHS hospitals had to foot the bill for the cleaning costs.
Responding to the criticism, health minister Ben Bradshaw said: "Once again the Tories have got their numbers wrong. Over £62 million from trust surpluses has been spent on a successful round of hospital deep-cleans.
"Deep-cleans are immensely popular with patients, the public and hospital staff. Far from being a 'gimmick', they are one of a series of initiatives we have delivered to make our hospitals cleaner and safer."