The government has been accused of misleading the public over its claim that all trusts would deep clean their entire sites.
The Department of Health announced last September that "hospitals have been asked to deep clean their entire sites, restoring surfaces and fabrics as close as possible to their original condition".
That month, prime minister Gordon Brown told the Labour Party conference he wanted trusts to deal with "a ward at a time", leaving "walls, ceilings, fittings and ventilation shafts disinfected and scrubbed clean".
But HSJ has learnt that trusts were given individual targets by strategic health authorities that focused on specific priority areas, rather than a wholesale clean across every ward.
In addition, a handful of trusts that responded to an HSJ poll last week, admitting they had not carried out the deep clean, were then reported by SHAs as hitting the target by the deadline on Monday.
Liberal Democrat health spokesman Norman Lamb said: "My understanding was trusts would have to go through the whole premises. What you have uncovered demonstrates the problem with this sort of centrally imposed approach. It was politically, rather than clinically, driven."
Ruth Boaden, professor of service operation management at Manchester Business School, said: "The public were misled by the words the politicians used." The money "would have been better invested in more ongoing cleaning", she added.
Twenty trusts are yet to complete the deep clean, according to SHA figures. The region with the most trusts missing the deadline was the North West, with six trusts, followed by London, with five. The South West, South East Coast and East Midlands said all their trusts hit the target.
An East Midlands spokesman said there was a "different target for each trust, going on what the priority areas were."
In February, Monitor executive chairman Bill Moyes wrote to NHS chief executive David Nicholson telling him the instruction encroached on foundation trusts' independence.
The programme was allocated£57m of SHA funding, but many have questioned its effectiveness.
Picker Institute head of policy and communications Don Redding called for a "cold appraisal" of whether deep cleaning should play a central part in infection control.
The DH is working with SHAs to see if there is a correlation between infection rates and deep cleaning, according to NHS Confederation deputy policy director Jo Webber.
A DH spokesperson commented: "We have made it clear that it is for individual trusts to agree and commission plans locally based on clinical need. In some cases this would mean an entire site clean, but this would be wholly dependent on local factors."