Health Secretary Alan Johnson warned today that the four worst-performing NHS Trusts face "radical action" - including a takeover - unless they improve.
Mr Johnson said he has asked David Nicholson, chief executive of the NHS, to "urgently meet" the four trusts to "assess what action they are taking to remedy the situation".
He said: "If this is not satisfactory, we will consider more radical action.
"Stringent assessments would need to be made regarding the most appropriate course of action but one of the options could be takeovers by well-performing trusts.
"I have also asked strategic health authorities to publish and implement action plans within 30 days for trusts who are weak on both categories.
"This helped improve poor performers last year."
Mr Johnson said the Healthcare Commission's report on the NHS trusts "was the toughest and most comprehensive assessment of the NHS ever".
"Our expectations are high and we expect NHS trusts to improve every year," he explained.
"That is why we set up the Healthcare Commission to assess every NHS organisation, carrying out inspections where necessary to ensure they meet high standards and deliver for their patients.
"This independent verdict on the NHS shows clear improvement, with more trusts getting an excellent rating, more trusts improving on last year's performance and fewer in the lowest category.
"The well performing and improving trusts are to be congratulated, particularly the 19 trusts that scored excellent on both use of resources and quality."
He added: "But we need to see more improvement from those classed as weak."
The four trusts affected are those judged to be "weak" in both parts of the commission's performance ratings - for quality of services and use of resources - in 2006/07 and 2005/06.
They are: the Royal Cornwall Hospitals NHS Trust, Northern Devon Healthcare NHS Trust, Surrey and Sussex Healthcare NHS Trust and West Hertfordshire Hospitals NHS Trust.
The commission's report found over a quarter of NHS trusts in England were
failing to meet new infection control standards to tackle superbugs like MRSA and Clostridium difficile (C diff).
It expressed "concern" that 111 of the 394 trusts assessed - 44 of them acute and specialist trusts - had not complied with one or more of three Government hygiene standards.
But the commission found trusts' performance was in general improving, with more scoring "excellent" and fewer scoring "fair" and "weak" when judged on quality of services and use of resources, or financial management.
The chief executive of the Royal Cornwall Hospitals NHS Trust, judged to have the country's worst record overall, acknowledged today that its standards were "not acceptable".
But John Watkinson said it had scored highly in some areas such as patient experience, saying 95% of people who used its hospitals found the care to be excellent, very good or good.
He told GMTV: "Patients support the hospital, but we have got to improve our performance and have already set out how we will try to do that."
Today's figures follow the commission's publication last week of its investigation into the outbreak of C diff which affected the Kent and Sussex Hospital, Pembury Hospital and Maidstone Hospital.
The commission said it was currently carrying out its biggest programme of hygiene inspections aimed at driving out hospital bugs.
The general secretary of the Royal College of Nursing, Peter Carter, said trusts had improved on infection control but standards needed to be higher.
He went on: "The lessons of the last few weeks prove that this issue is literally one of life and death.
"For us to tackle healthcare-acquired infections, staff need to be fully supported, the right resources have to be in place and responsibility must be shared from the board to the ward."
In all, one in three trusts in England improved on quality of services and a similar number did so on use of resources, the commission's annual health check for 2006/07 found.
Overall, 19 NHS trusts scored "excellent" on both parts of the rating, up from two last year.
On quality of services, 16% of trusts were "excellent" and 30% were "good".
But the commission said it noted "with concern" that 33 trusts (8%) were rated "weak" on quality of services.
Of these, 20 were "weak" on both parts of the rating, four of these for two years running.
Anna Walker, chief executive of the Healthcare Commission, said it had been a "tough" year for the NHS with significant reorganisation taking place, and tougher standards on infection control.
She said: "Many trusts have stepped up to the challenge. They have delivered improvements in areas that really matter to patients, such as waiting times."
Responding to today's report, shadow health secretary Andrew Lansley said: "Many NHS professionals work hard to meet standards and there have been notable improvements like the reduction of cancelled operations.
"But despite extra funding, the NHS still faces significant difficulties such as the failure to reduce MRSA.
"Patients should be rightly concerned that the report doesn't even measure C difficile rates."
Liberal Democrat health spokesman Norman Lamb said: "Progress on Government targets must not come at the expense of the most important priority of all: clean hospitals free from infection."
Niall Dickson, the chief executive of health think-tank the King's Fund, said: "It is of particular concern that one in four trusts are classified as 'weak' when it comes to the efficient use of resources and over a third are classified as only 'fair'.
"The days of massive spending rises are coming to an end - that makes improved productivity absolutely key to better services. Low productivity threatens the long-term sustainability of the NHS."
He added: "Reports like this are useful in giving patients and others information about performance and standards, but that is just the first step.
"Only when patients are given the power to use the information to decide, along with their practitioner, what is best for them will the NHS be able to say it is delivering truly personalised care."