Health trusts in England are more than £1bn in debt, a major investigation by the BBC News website has revealed.
Ms Hewitt insisted only a quarter of NHS organisations were in debt
Every NHS trust or primary care trust in England was asked for its current financial situation, whether it was in debt or had money in the bank.
The total for the whole country showed a debt of £1.07bn - despite the NHS receiving record funding of £76.4bn for the financial year 2005-2006.
It has led to patient services being affected as trusts try to cut spending.
Some trusts revealed they had closed beds, wards or entire hospitals, others had cancelled operations and many said they had cut staff levels.
The government has forecast the NHS as a whole in England will be £620m in debt by the end of the financial year in March.
Health Secretary Patricia Hewitt told BBC News: "Three quarters of local NHS organisations are balancing the books or in surplus."
But in the BBC survey more than half the trusts indicated they were in debt, although some of those did forecast they would break even by the end of the financial year.
Some of those who said they would cut or eliminate their debts by the end of March said their cuts would have no impact on patients.
But others did reveal more drastic action, such as closures, redundancies or cancelled surgery.
Ms Hewitt announced on Wednesday 18 trusts with financial problems would be given "turnaround support" - help from financial experts to help them tackle their problems.
Another 23 organisations will be monitored by regional NHS management to make sure their deficits are eased.
Ms Hewitt said: "I have announced decisive action to turn around the minority of NHS organisations which have significantly overspent their budgets.
"This government will have trebled the investment in the NHS - and we are ensuring that every penny of extra cash is spent wisely for the benefit of patients.
"Throughout the country people can see that our investment means extra doctors and nurses, quality treatment and faster access to health services."
Much of the debt is centred on London and the Home Counties, with deficits in the capital alone accounting for almost a quarter of the total across England.
Hammersmith Hospital NHS Trust reported the biggest single deficit
The largest single reported debt for any one health trust was for the Hammersmith Hospitals NHS Trust in London.
It has a debt of £16.2m, but also runs Ravenscroft Hospital for the Department of Health, which has a debt of £19.1m - making a total deficit for the trust of £35.3m.
Management said they had taken a wide range of steps to reduce the debt - including cutting 300 jobs.
The John Radcliffe Hospital in Oxford announced in December that many patients would not be able to have the same heart therapy received by Prime Minister Tony Blair, with only life-threatening conditions still being treated.
The withdrawal for up to 100 patients of cardiac ablation therapy, to control an irregular heartbeat, was blamed on the need to cut Oxfordshire's £15.1m deficit.
Ms Hewitt criticised the trust's bosses for failing to manage their budget effectively - and the trust is not one of the 18 to be given turnaround support.
Ms Hewitt told the BBC: "Improving financial management does not mean compromising services for patients.
"Any action that the NHS takes to reduce deficits should not lower the quality of care provided to patients."
Several organisations have expressed their concern at the level of debt in the NHS, or the way it was being dealt with.
Michael Summers, chairman of The Patients Association, said: "Those that have very large deficits do affect patient care, it's very clear.
"It is very worrying at the moment.
"Looking at it optimistically, in the new financial year hopefully things will get better, but it is not going to happen overnight."
The Royal College of Nursing said earlier this month it feared more than 3,000 health service jobs could be lost through cost-cutting efforts which were having a "direct and detrimental" effect on patients.
Unison, the trade union which represents many nurses, said newly-qualified staff were struggling to find jobs because posts were being left unfilled.
And the NHS Confederation, which represents more than 90% of NHS organisations, said trusts were under too much pressure to cut deficits quickly and needed to be given "space" to deal with debt in a way which had patients' care at heart.