It found that 20 trusts were not meeting minimum standards for balancing the books and 12 of these had failed to do so for three consecutive years.
However, the report also concluded that although the NHS in general is improving the way it handles the money it is given by government it must to do more for patients who it said 'deserve better'.
Overall a previous £547m NHS deficit has been turned into £1.7 bn surplus this year however Audit Commission chairman Michael O'Higgins said that 'pockets of real concern remain. Poor financial management can put services for patients at risk.
'Patients and the public deserve better from the poor performers and we should be seeing a lot more,' he said.
Chief executive of the Royal College of Nursing Peter Carter welcomed the improvement in the NHS overall financial situation.
'This is a clear recognition of the hard work of nurses and all frontline NHS staff who have made wards more productive'.
However, he warned that trusts in surplus meant money was not spent on frontline staff and patient care.
'Every penny of the record £1.7 bn NHS surplus must be spent on enabling frontline staff to spend more time by the bedside caring for patients'.