The NHS in England will be £750m in the red by the end of the financial year on 31 March, a BBC survey suggests.
Ministers have denied NHS chief Sir Nigel Crisp quit over the figures
BBC Two's Newsnight asked all 28 strategic health authorities, which control most of the NHS's £76bn budget, for their latest forecast deficits.
Twenty predicted deficits totalling £799m, while a handful of surpluses brought the net deficit to £750m.
The figures came after ministers this week denied NHS chief executive Sir Nigel Crisp quit over the situation.
Strategic health authorities handle budgets for hospitals, GP surgeries, community health programmes, mental health and ambulance trusts.
Newsnight also contacted all 32 foundation hospital trusts, which are funded separately.
Overall they were £10m in the red, making the total NHS deficit £760m - or about 1% of its budget.
Sir Nigel on Tuesday announced he was stepping down, saying "not everything has gone well" and sparking reports he had been pushed out.
Downing Street denied he was "carrying the can" for financial problems in the NHS.
The Tories said his "rushed" departure was a clear admission of a crisis.
Some of the largest health authority deficits are:
- North West London - £106m
- Surrey and Sussex - £102m
- Norfolk, Suffolk and Cambridgeshire - £89m
- Bedfordshire and Hertfordshire - £85m
- Shropshire - £49m
- Hampshire and the Isle of Wight - £44m
- South East London - £40m
The new interim chief executive of the NHS, Sir Ian Carruthers, who is replacing Sir Nigel Crisp, is currently in charge of two health authorities - one predicting a deficit and one a surplus.
Hampshire and the Isle of Wight is forecasting a deficit of £44m, while Dorset and Somerset is predicting a small surplus of £6.5m.
Health Secretary Patricia Hewitt has refused to say how much she expects the total NHS deficit to be, although she conceded it would be larger than the government's £200m target.
The half-year forecast in December was £623m.
Earlier this week she said that only "a very small minority" of hospitals and NHS bodies had serious financial problems.
Health minister Caroline Flint told Newsnight the government wanted to know why some authorities were not managing their finances as well as others, with 50% of the deficit being in 6% of the organisations.
"Sometimes it's our poorest areas, with some of the most difficult health challenges, that are managing their finances but also producing results better than the more affluent areas," she said.
Dame Gill Morgan, chief executive of the NHS Confederation, which represents 90% of NHS organisations, said many of the organisations with debt had had it building up for some time.
"We need to work alongside the organisations to try and help them turn around," she said.
David Nicholson, chief executive of three authorities in the West Midlands, with a combined deficit of £70m, said there were "serious difficulties" in front of them.
"I don't think it's a matter of closing hospitals... the first and most obvious thing we need to do is bring proper financial management into some of these organisations," he said.
Some debt-ridden authorities needed help as they were "grappling with really quite serious problems", he said.