NHS Foundation Trusts have said that they are experiencing increased financial pressures and may not meet waiting times this year, according to the regulator Monitor.
21 Trusts expect to experience financial problems this year, up from 13 last time they were surveyed.
16 Trusts added that they risk failing to treat patients on time, with a similar number expecting to breach A&E waiting time targets.
Foundation trusts are the top-performing organisations in the NHS. Monitor, the regulator for the semi-independent Foundation Trust sector, is advising that they avoid cutting patient care to meet the Government's savings target of £20 billion by 2015.
Dr David Bennett, Chairman of Monitor, said: "The challenge of reducing costs must be met, but it is essential that good patient care is at the heart of this. This year we have put extra focus on identifying the potential risks to quality that could result from each Trust's plan.
"The evidence we have seen in foundation trusts' plans suggests they are not planning to make savings by treating fewer patients or reducing the level of care for patients. Instead they plan to make them through more efficient working on the front line and by reducing administrative or clerical costs."
Most Challenging Time
A report by Monitor published today analyses the three year plans of all 137 Trusts, suggesting they now face their "most challenging time".
Operating expenses are increasing and managers must make savings of 4.4 percent, with most planning to cut staff costs to achieve targets.
The highest or second highest financial risk rating has been given to 11 Trusts, up from four last year. An additional ten Trusts expect to experience financial problems at some point in the year.
Although the Trusts are currently set to meet Government cuts targets, it is expected that increases in spending on drugs and the added cost of Private Finance Initiative deals to build new sites will strain their budgets.
A spokesperson for the Department of Health said: "This Government is investing an extra £12.5 billion in the NHS. But increasing demands on services also mean we have to modernise the NHS if we want to sustain it and improve the quality of patient care.
"Our NHS bill strengthens the foundation trust model, ensuring that all hospitals are fit for the future. This report shows foundation trusts are prepared for the challenges ahead."
The Government target treatment time for patients of within 18 weeks of referral looks set to be broken by 16 Trusts, while 14 Trusts are set to breach the four hour A&E waiting time and this number may increase during winter.
Levels of the superbug C.difficile will likely not be kept as low as required in 16 Trusts.
A spokeswoman for the Department of Health added: "Foundation trusts have greater autonomy to innovate new ways of delivering health services - they are truly responsive to patients, not ministers.
"But their freedom comes with responsibility and foundation trusts must demonstrate that they are improving outcomes for patients and managing their finances effectively as well as ensuring that waiting times are kept low."
John Healey, Shadow Health Secretary, said: "David Cameron claims that his reckless NHS reorganisation will help the NHS deliver more efficient services. However, we now know that it is distracting the NHS from delivering challenging efficiency savings targets, with the NHS now facing a potential £1 billion black hole in savings."