"This report shows clearly that, for all the rhetoric, money is still moving into hospitals, not out of them," said co-author and Nuffield Trust Chief Economist Anita Charlesworth
"At the same time, however, we should recognise the success of PCTs in moving some care into the community,"
The proportion of hospitals in deficit has risen steadily over the last four years, according to the report.
Last year 32 trusts out of 250 were in deficit and nine reported a deficit for over three years.
Dr Peter Carter, chief executive and general secretary of the Royal College of Nurses (RCN) said: "We are concerned about the mixed picture of some trusts being financially healthy while others are consistently on the edge.
"Nurses will be very worried that hospital trusts which have to focus on finance may struggle to maintain good, quality care."
2011/12 was the only year PCTs did not spend all the money allocated for commissioning.
However, the report claims this is because in 2011/12 learning difficulties provision was transferred from PCTs to local authorities.