Jeremy Hunt has inflamed the dispute with junior doctors by insisting “the matter is closed” and he will impose the new contract on them, despite unprecedented protests by medics.

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The health secretary also insisted that history would judge him right to force new terms and conditions on England’s 45,000 junior doctors, despite the wave of concern across the NHS and medical profession that his move has triggered.

“The matter is closed. We have been trying to discuss this now for three years, and I think the wrong thing to do in the face of unreasonable behaviour is to say, ‘Well, in that case, we’re going to back down,’” the Health Service Journal (HSJ) reported him as saying.

His comments emerged [see footnote] as medics below the level of consultant took part in the second day of their fourth strike against the new contract, which is scheduled to come into force in August. Hospitals said that 42.5% of junior doctors had turned up for work on Thursday, a lower number than the 46% who did so on Tuesday.

Hunt said the planned new contract was “much safer” than the current one. He added that he was “more in tune with doctors” than the British Medical Association (BMA), their union, “because I really care about the things that doctors care about – the safety of patients”.

The health secretary was speaking at an event held last month and organised by the HSJ.

“It’s inevitable when you are painted as the evil bogeyman by the BMA, who are brilliantly clever at winding everyone up on social media, that you are not going to be Mr Popular,” he said. “But what history will judge in five or 10 years’ time is, did I and did this government make the long-term strategic calls necessary to help the NHS offer the highest possible quality of care for patients?”

There is growing frustration from patients about the cancellation of appointments and alarm about the threat of junior doctors withdrawing cover from all areas of care, including A&E, on 26 and 27 April.

The Department of Health said 5,156 procedures and operations had been postponed as a result of this week’s 48-hour strike, which is set to continue until 8am on Friday morning.

Junior doctors are providing emergency care only in the fourth stoppage in their long-running dispute with the government over a new contract. They plan to escalate the dispute on 26 April with another two-day strike, including a walkout from casualty units.

Dr Johann Malawana, who chairs the BMA’s junior doctors committee, accused the government of failing to prevent the latest strike. Hunt has refused to discuss the strike since it began on Wednesday.

Patients who have had tests and operations cancelled urged both sides to return to the negotiating table. Lee Caller, from east London, blamed Hunt and the BMA for an “anxiety-ridden week” after his cancer diagnosis was delayed because of the strike.

Gill Shaw from Wokingham in Berkshire said her mother’s heart operation had to be cancelled, despite being described as urgent. Speaking to BBC News she said: “I think the discussions should reopen. I think the doctors should communicate better to patients why things are being cancelled when they’ve been described as urgent.

“That’s when families and patients become distressed and find it difficult to reconcile the disruption and strike action with their needs. What happens if my mum doesn’t make it to the operation?”

Shaw also expressed alarm about the BMA’s threat to withdraw emergency cover. “I’m very concerned about the A&E walkout. What happens if we have a [terror attack like] Brussels? They really need to start the conversations again, they have to.”

Isabel Barnard, from south-east London, said she was distressed and annoyed after a biopsy appointment for rare liver disease was cancelled because of the strike. “It is not fair on us awaiting urgent procedures and tests,” she told the BBC. But she added: “I doubt the politicians proposing this would be happy if they were to work the additional unsociable hours with no extra pay, so I can understand their [doctors’] reasons for being so angry.”

Asked about the threatened A&E walkout, she said: “That’s going to have a detrimental effect. I really don’t think junior doctors should take that strike there, but I can understand why they have got to do something for themselves.”

Nick Hulme, chief executive of Ipswich hospital NHS trust, said the impact of the walkout on patients was increasing. “This is the fourth strike that we’ve had, so the cumulative effect of patients’ [appointments] being cancelled, their families being disrupted is starting to have an effect on the hospital as a whole,” he told BBC Radio 4’s World at One programme.

“It is not getting any easier and as these strikes escalate into the full walkout in three weeks’ time, clearly, I am becoming increasingly concerned about that. We are working up our contingency planning, but clearly taking junior doctors out of A&E, ICU [intensive care units] and maternity services does cause significant risk and, though I’m confident we will be able to safely manage patients, it will require consultants, nurses, therapists, other doctors to work very differently.”

The major sticking point in the dispute has been over weekend pay and whether Saturdays should attract extra unsocial hours payments. Currently, 7pm to 7am, Monday to Friday, and the whole of Saturday and Sunday attract a premium rate of pay for junior doctors.

• The following footnote was added on 8 April 2016: Jeremy Hunt’s remarks were reported in the Health Service Journal’s weekly print edition dated 6 April 2016, but had previously been reported on the publication’s website on 23 March.