The government's strategy for halving the number of hospital superbug infections was in disarray yesterday after a leaked internal memo to Patricia Hewitt, the health secretary, revealed doubt as to whether the target could ever be met.

Liz Woodeson, the director of health protection, warned Ms Hewitt that the three-year target to halve MRSA infections by April 2008 was likely to be missed. "Although the numbers are coming down, we are not on course to meet that target and there is some doubt over whether it is in fact achievable," she wrote in October.

The memo, leaked to the Health Service Journal, suggested a range of options for breaking the bad news to the public. Option one was to keep the target, for which the government would be criticised. Option two was to drop it, for which it would be "difficult to get No 10 agreement" and "handling would be extremely tricky given the high media interest in 'superbugs'". Option three would extend the deadline for a year, but the memo said: "We would be open to the accusation of fiddling the target because we knew we weren't going to achieve it."

The document also expressed concern about a different bug, Clostridium difficile, which causes more illness and death than MRSA. "Although there have been some high-profile outbreaks - most notably at Stoke Mandeville - it is endemic throughout the health service with virtually all trusts reporting cases," it said.

Scientists lined up to agree with the memo yesterday. "My view is that it is not surprising that the MRSA target will not be met - I haven't met anyone in the health services who ever thought it was achievable," said Dr Mark Enright, senior research fellow at Imperial College.

"The fact that MRSA infections are out of control should come as no surprise," said Dr Ronald Cutler, principal lecturer in infectious diseases and pathology at the University of East London. "Carriage and spread from wound infections, staff to staff, patient to patient in hospital environments is still a major problem and other potential 'hotbeds of infection' such as nursing homes remain a relative unknown. Current control, hygiene and rapid MRSA detection methods have failed to stop this organism."

It was always accepted that MRSA could not be eradicated from hospitals, not least because some patients arrive already infected. About a third of the population carry Staphylococcus aureus on their person harmlessly and MRSA is a variant of this which will not respond to the antibiotic methycillin, normally used to treat wound infections.

But the NHS is 27% off the trajectory it should be on if it is to halve infections. Some trusts will not reach the target because they have large wards and few single rooms where they can isolate patients. For this and other reasons, such as that 20% of elderly people arriving from nursing homes have MRSA already, the memo said, "the opinion of DH infection control experts is that we will succeed in reducing MRSA bloodstream infections by a third, rather than a half - and that even if we had a longer period of time it may not be possible to get down to a half".

The Patients Association said the risk of infection with a superbug was the biggest worry for patients going into hospital. "By failing to insist on the NHS getting a grip, the situation has been made worse ... Even their own 'clean your hands' campaign has disappeared," it said.

Andrew Lansley, the Conservative health spokesman, said staff were being misled by a target in which the Department of Health did not believe and called for a "search and destroy strategy" to fight MRSA. The Department of Health deplored the leak and said the government was committed to the target. "Progress towards a 50% reduction of MRSA bacteraemia has been slower than anticipated and although numbers of MRSA bloodstream infection are coming down, faster progress is needed to meet the target," it said in a statement.

FAQ: Superbugs

What is MRSA?

It is a form of very common bacterium, Staphylococcus aureus.

Can it be treated?

Yes - but there are only a couple of antibiotics that will work.

Is it the only hospital superbug?

No. Several are now causing concern. There were 1,300 deaths caused by Clostridium difficile in 2004.

Should medical staff wash their hands more often?

It's part of the answer, but not enough by itself. Antibacterial wipes are effective against MRSA but not against C difficile.