The NHS is in good financial health after producing a surplus of £1.5bn over the last financial year but it faces a stiff challenge over the coming years.
Only nine of the 276 NHS organisations failed to balance their books, although some required financial assistance to do so, the Audit Commission report showed.
It added that almost a quarter of NHS trusts (27 in total) and 12 % of PCTs (18) received qualified value for money conclusions.
The NHS Confederation said NHS leaders are starting out from a strong position to achieve the £20bn savings required of them, but pressure will increase in the years to come.
Jo Webber, deputy director of policy at the body, said: "These figures show that many NHS leaders have got their organisations on a strong footing to achieve the £20bn savings required of them.
"But they are worried that this could be the calm before the storm.
"Many of our members have told us they are expecting the financial situation facing their organisations to be the worst they have ever experienced."
In June the Confederation surveyed 287 chief executive and chairs across the NHS and found 82% did not expect to overspend their budgets during the next 12 months.
However, 42% said the financial situation facing their organisation was "the worst they had ever experienced", while an additional 47% said it was "very serious".
More than two thirds of those surveyed thought financial pressures would increase over the next three years (67% over three years, 70% over the next year), with 39% saying it would "increase significantly".
