The Department of Health revealed yesterday that there had been almost 45,000 cases of a virulent bug last year, killing nearly three times as many patients as MRSA.
The hospital-acquired bacterium Clostridium difficile was found to be the cause of death in 934 people, most of whom were old and frail.
Charities and opposition politicians blamed the government for giving inadequate priority to hospital hygiene, but the department said its decision to publish the facts was an indication of its commitment to raising standards.
Officials said 44,488 patients, most of them over the age of 65, had been infected by the bacterium in hospital in England last year, up by 25%.
This compared with 7,683 patients who were infected with MRSA, which was the underlying cause of 321 deaths.
The department said C. difficile was the main cause of antibiotic-associated diarrhoea and colitis.
The bacterium can be found in up to 5% of healthy adults, but is kept in check by the intestine's normal "good" bacteria. When these bacteria are knocked out by antibiotic treatment for another condition, C. difficile multiplies and produces damaging toxins.
While most patients make a full recovery, the infection may be life-threatening to older people with other illnesses.
The control of hospital acquired infections has become a priority for medical staff and a headache for ministers.
The NHS was put on full alert about the dangers of C. difficile after an outbreak of a virulent strain at Stoke Mandeville hospital in Buckinghamshire, which has infected more than 300 patients since 2003. It was disclosed in June that 12 patients with an average age of 85 had died after being infected with this strain.
In a league table published yesterday, Stoke Mandeville emerged with a relatively low rate of infection. George Eliot hospital NHS trust in the west Midlands had the highest.
Its medical director, Peter Handslip, said the characteristics of the local population could influence the results. "North Warwickshire has a proportionately large elderly population and the elderly are increasingly susceptible to this sort of bug," he said.
The department also said there had been 620 cases of glycopeptide-resistant enterococci infection in England, but no deaths attributed to it.
Christine Beasley, the chief nursing officer, said the increase in infections was partly due to a rise in the number of patients needing antibiotics.
"We added C. difficile and GRE to the mandatory surveillance system to help the NHS establish the scale of the problem and ... help improve infection control," she said.
Karen Jennings, of Unison, said hygiene had to be improved. "It's not rocket science - the way to wipe out these superbugs is to have cleaner hospitals and if you want cleaner hospitals you must have more cleaners."
Simon Burns, the Conservative health spokesman, said superbugs were proliferating. "The first steps to cleaner hospitals are to scrap Labour's political targets and put matron in charge," he said.
Patricia Hewitt, the health secretary, is to publish legislation towards the end of October making chief executives responsible for cleanliness.
