Hospitals are warning that fines for missing targets are in danger of threatening patient care.
Under NHS rules trusts can be penalised for not hitting targets such as the four-hour A&E waiting time mark.
An investigation by BBC Radio 4's You and Yours programme found some trusts were fined over over £8m last year.
Hospital bosses said fines were counterproductive, but local managers insisted they were a useful tool to drive up standards.
You and Yours asked 164 hospital trusts in England about how much they had been fined. Of the 97 which responded, 46 had not been fined at all.
But of the remaining 51, the fines levied by local managers totalled £92m. The trust fined the most was Kings College Hospital NHS Trust which paid £8.4m in fines. The next highest was University Hospitals of Leicester which paid back £7.7m.
The largest number of fines - nearly £30m worth - were levied on hospital trusts for missing their 18-week waiting time target for routine operations like knee and hip replacements. A&E fines totalled nearly £18m.
Chris Hopson, chief executive of NHS Providers, which represents 200 NHS trusts, said: "We're not arguing that providers should get a free pass but fines are neither the best nor the only method for changing practice, particularly when they are often applied to issues that are beyond providers' control.
"We also view the increase in fines as ultimately reducing providers' ability to hire staff and fund service improvements, and that such a rise is therefore counterproductive to enabling the best quality care."
Stephen Conroy, chief executive of Bedford Hospital NHS Trust, was fined £2.8m for the last financial year. He said: "In the first week of January when there was a national problem of more patients turning up in A&E. We had to cancel every elective operation because we had so many people in A&E waiting to be treated and to have beds.
"We worked really hard to turn things around but then we got fined for ambulances queuing up to deliver patients, we got fined for not hitting the 18- week target to treat people because we cancelled those operations.
"When you are in crisis like that the fines provide no incentive at all. When you get overwhelmed normal business doesn't apply. There is no way the targets can provide any incentive for us to treat people any differently. All they do is make your financial position worse and make it harder."
Julie Wood, director of NHS Clinical Commissioners, which represents local managers, defended the system: "These fines are not about a trust paying back money to deliver, it's about withholding money when a trust has failed to deliver against a statutory mandatory performance standard.
"The money is held to reinvest in care and services that will help that local place to deliver those standards. It is not about money going back to the Treasury but reinvesting it in front line services to help the local system deliver against the national standards."