The deep cleaning is part of a strategy to reduce superbugs
The NHS is likely to narrowly miss its target to deep clean all the hospitals in England by the end of March.
Ministers expect 93% of trusts to have completed the process by the end of Monday. The rest have all started the cleans and will finish soon, they say.
But the Tories said it was a shambles as not all the money promised to cover the costs of cleaning had materialised.
A total of £60m has been spent on cleaning but the Tories say just £15.6m has gone to hospitals to pay for it.
The Tories obtained the data on the cleaning of all 1,500 acute, district general and community hospitals in the country under the Freedom of Information Act.
News of the financial shortfall between the money released to hospitals by regional health authorities and the actual cost of the deep clean comes amid mounting criticism of the programme since it was announced last year by the prime minister.
Infection control experts have dubbed the programme a gimmick, claiming it will only have a short-term impact on hospital infections such as MRSA.
Dr Jodi Lindsay, an expert in infectious diseases, told the BBC the programme had inherent flaws.
"The reason that it's not going to work is that MRSA is carried by people and as soon as you deep clean a hospital, if you let people back into it again, you're going to have the same MRSA problem," she said.
Cleaning firms have said the government should instead have properly funded day-to-day cleaning.
'Package of measures'
But health minister Ben Bradshaw hailed the exercise as a success. ''We expect 13 out of 170 hospitals to miss Monday's deadline," he said.
"Only four of those don't expect to finish their deep clean by April and they may have good reasons for it - such as undergoing building work, for example."
He said it was important to recognise the deep clean was part of a package of measures which was having a dramatic effect on bringing down infection rates and that is what matters to the public.
"MRSA is down 35% this year; C-difficile down 16%. And rather than constantly knocking the NHS I do think its about time we congratulated staff for achievements like that.''
HAVE YOUR SAY
Who isn't worried? Hospitals in my experience are filthy. They don't even smell sanitized and hygenic anymore
KA Owen, Bristol
Extra infection control nurses and MRSA screening also form part of the government's strategy to fight infection.
Andrew Large, of the Cleaning and Support Services Association, which represents the firms responsible for carrying out the deep cleaning, said there were two main reasons for hospitals missing the deadline.
"Some have had a problem freeing up wards of patients to allow the cleaning to take part.
"However, some others have actively decided not to rush the process. They will all get there in the end, I am sure."
But shadow health secretary Andrew Lansley branded the programme a "shambles".
"It is appalling that Gordon Brown has broken his promise to fund it and now the local NHS has ended up footing the bill," he said.
He also questioned how effective it would be in the long run.