And it added while paying consultants for additional work was "essential" to cut waits and provide safe care, the NHS was "committed to spending taxpayer money wisely".
Meanwhile, Health Secretary Wes Streeting said he agreed the rates were not acceptable, adding: “Every penny that goes into the NHS needs to be well spent."
But the British Medical Association (BMA), the doctors' union, pointed out the NHS would not have to rely so much on overtime were it not for staffing shortages.
NHS Frimley Health Foundation Trust paid two consultants in its endoscopy department, which provides internal examinations, more than £180,000 each in overtime, to tackle the backlog in treatment.
The trust said: “We’re focused on ensuring we always provide value for money - and anything we spend is in proportion with the benefit it brings to our patients.”
NHS Humber Health Partnership, which runs five hospitals, paid three consultants between £185,000 and £240,000 in overtime.
Chief medical officer Kate Wood said the overtime spending had helped fund extra operations at weekends, to reduce waiting lists.
“We assess the costs of these shifts against the risks of not having cover," she said.
"We have put patient safety first as that is our key focus.
"This is not something that is unique to us.”
Worcestershire Acute Hospitals NHS Trust paid three consultants more than £100,000 in overtime, including one who earned just above £198,000.
Managing director Stephen Collman said the trust was trying to reduce “premium payments” where possible but the need to cover sickness absence and vacant posts meant to keep services “running safely and effectively” it had no option.
Some hospitals said overtime rates had been driven up over the past year by the particularly high rates the BMA had told its consultants to ask for to provide strike cover.
"It created a new expectation of what they should get," one official said.
But BMA consultant co-leaders Dr Helen Neary and Dr Shanu Datta said: “Unfortunately, a declining workforce in crisis and spiralling patient demand - which has led to sky high waiting lists - means that extra hours of work are essential to get the job done.”
They pointed out much of the overtime was done during unsocial hours, adding these were “highly-trained and experienced professionals” so it was reasonable for them to value their time “at appropriate rates”.
Danny Mortimer, of NHS Employers, which represents hospitals on employment issues, said: "In light of the difficult financial position of the NHS, health leaders are trying to bear down on extra-contractual premium pay rates."
But there were no easy solutions as consultants played a "critical role" in tackling waiting lists.