The deadly Clostridium difficile hospital bug is on the rise, while MRSA superbug rates are falling too slowly to meet government targets.
C difficile rates are on the rise
The Health Protection Agency figures show the C difficile rate rose by 5.5% in England during the first three quarters of 2006 to 42,625.
The MRSA rate fell by 5% to 3,391, but if trends continue the target of halving cases by 2008 will be missed.
HPA officials said there was still much to be done to get a grip on the bugs.
Dr Georgia Duckworth, a hospital infection expert at the HPA, said: "While there are some encouraging signs in today's figures, there clearly remains much to be done.
"Cases of Clostridium difficile infection continue to rise - there may be some slowing down in the rate of increase, but it is too early to say for sure.
"With MRSA rates we are still seeing a plateau rather than any significant decrease, but the good news is that we can now say with confidence that reported rates are no longer rising."
In November 2004, then health secretary John Reid pledged MRSA rates would be halved by April 2008.
But a leaked government memo, sent to ministers by a Department of Health official, has predicted it would only be cut by a third by then.
Ministers have asked NHS trusts to set their own targets to reduce C difficile rates.
Healthcare Commission Chief Executive Anna Walker said: "It's disappointing that trusts have not been able to make more progress, more quickly on reaching the target for 2008."
And Graham Tanner, of the patients group, the National Concern for Healthcare Infections, said: "It should be remembered that each of these statistics represents a person and family who suffer the contraction of a healthcare infection that they probably did not have on admittance to hospital.
"Sadly in a large number of cases people will have lost their lives as a consequence of these infections."
The HPA did not look at deaths although figures from 2004 show that MRSA was mentioned on over 1,000 death certificates in England and Wales, while C difficile was listed on over 2,000.
Health Minister Lord Hunt said: "The NHS has been working hard to tackle infections and I commend those trusts that are showing improvement."
He also revealed that NHS trusts had applied for 90% of a £50m government fund to help hospitals install new facilities to tackle infections.
However, Professor Richard James, director of the Centre for Healthcare Associated Infections, University of Nottingham, said the government's recommendation for universal screening of all new hospital admissions for MRSA was unfeasible.
He said: "NHS microbiology laboratories are under-resourced to be able to take on this task which involves the adoption of new molecular diagnostics technology."
Professor James also stressed that the MRSA figures related only to blood infections and were therefore only a small percentage of the total MRSA infections in hospitals.
Andrew Lansley, the Shadow Health Secretary, said: "Conservatives have stressed the need for urgent action to tackle the C. difficile infection in our hospitals.
"Patients are being put at risk, yet the government seem intent on ignoring the reality that C. difficile, like MRSA, is now endemic in hospitals."
Members of the MRSA support group will meet Lord Hunt on Tuesday to call for more action on superbugs.
They say the NHS is guilty of "chronic inertia" and are calling on the government to consider a raft of measures aimed at combating the problem.
C. difficile is a bacterium found in the gut of up to 3% of healthy adults and 66% of infants, where it rarely causes problems.
However, it can cause illness when its growth goes unchecked. For example, treatment with certain antibiotics can disturb the balance of "normal" bacteria in the gut, allowing C. difficile to thrive.
It can cause mild or severe diarrhoea, or in some cases severe inflammation of the bowel which can be life threatening.
MRSA stands for methicillin-resistant Staphylococcus aureus, but is shorthand for any strain of Staphylococcus bacteria which is resistant to one or more conventional antibiotics.
MRSA infections can cause a broad range of symptoms depending on the part of the body that is infected. These may include surgical wounds, burns, catheter sites, eye, skin and blood.