The government introduced a cap on sums paid to locum workers, but it can be breached by NHS bosses if they consider there is "significant risk" to patient safety.
The Royal College of Nursing (RCN) said it exposed "poor workforce planning" but said trusts had put safety first.
NHS Improvement said the cap had saved £300m.
The cap was introduced in response to a "very significant financial challenge" facing NHS providers, the health watchdog Monitor, part of NHS Improvement, said.
When the rules took effect Health Secretary Jeremy Hunt said staffing agencies had been able to "rip off the NHS by charging extortionate hourly rates".
The cap, which came into force in November 2015, set a limit on hourly rates for agency doctors, nurses and other clinical and non-clinical staff.
They started at 150% on top of normal pay for junior doctors and 100% for other staff, before gradually being reduced to 55% across the board from 1 April 2016.
In the first week that the rules first took effect, beginning 23 November 2015, the clause was used 35,662 times between 228 hospital trusts.
This fell to 21,277 times in the week beginning 28 December. Since then use has risen, reaching 54,419 uses in the week beginning 4 April 2016 and 53,644 in the week beginning 11 April, the last week of figures released.
The figures released by Monitor under the Freedom of Information Act suggest that, as the limit has come down, more staff have been affected.
The cap on pay for agency and locum staff was in response to hospitals "over-spending" on temporary workers.
The chief executive of NHS England, Simon Stevens, said in 2015 that he wanted to see the £1.8bn spent on agency and contract staff the year before turned into "good, paying permanent jobs". And he accused staffing agencies of "ripping off" the NHS.
Rising use of agency workers was partly down to hospitals putting more nurses on wards in the wake of the Stafford Hospital scandal, Mr Stevens said. The official report into the Mid Staffordshire NHS Foundation Trust identified a key reason for inadequate care was a lack of nurses.
However, the Royal College of Nursing says the NHS has not taken on enough student nurses to meet demand, resulting in agencies filling the vacuum and charging more to do so.
The health regulator NHS Improvement said hospitals in England were 15,000 short of the required number of nurses.
Figures obtained by the BBC in February 2016 showed there were more than 23,000 nursing vacancies in the NHS in England, Wales and Northern Ireland - about 9% of the workforce. That compares with a typical vacancy rate across all forms of work of 2.7%.
Details of each trust's use of the clause are recorded anonymously.
In the last week for which figures were available one hospital trust used the clause 1,310 times. Nursing, midwifery and health visitor staff made up 759 of those. Four other trusts also used the clause more than 1,000 times in the same week. Only 18 trusts did not use the clause at all in the week beginning 11 April.
Janet Davies, chief executive of the RCN, said: "Agency cap breaches are a barometer of the scale of the NHS's workforce problem, and it shows clearly that the problem is getting worse.
"NHS Trusts are unable to recruit nurses and are rightly prioritising patient safety over sticking to the cap.
"This is a workforce planning issue. The number of nurses being trained in the UK has been reduced, for short-term financial reasons."
A spokeswoman for NHS Improvement said the cap had saved up to £300m since October.
She added: "We know that trusts will need to override the cap where patient safety is a concern and it's important that they are able to do that. But as the new rules set in, whilst overrides did increase temporarily, they have begun to steadily decline as we expected.
"Overuse of agencies is bad for patients, bad for the NHS and unfair on other staff. These measures will help those staff currently working in agencies to come back into the NHS. Average prices paid for agency nurses have fallen by around 11% since October, so NHS nurses can be assured that their agency colleagues aren't being paid over the odds for doing the same job."
The biggest use of the clause came in a week when one of the junior doctors' strikes took place.
However, figures for other weeks when doctors were on strike in the long-running dispute over new contracts do not suggest a link as they were either less than the week before or rose in line with a general trend.
Rules on the amount hospitals can pay agency staff are being flouted more than 50,000 times a week, figures show.