Health secretary Matt Hancock on Thursday hit back at Dominic Cummings, denying he lied to Boris Johnson and saying the government had been better run since the departure of the prime minister’s former chief adviser.

After trenchant criticism by Cummings, Hancock blamed “clinical advice” for his decision to authorise the discharge of people infected with coronavirus from hospitals to care homes. It served to spread Covid-19 in care homes, where tens of thousands died.

And giving evidence to two House of Commons select committees investigating the UK’s response to the coronavirus pandemic, the health secretary defended the government against criticism that it had been late to introduce its first lockdown in March last year. Cummings claimed tens of thousands of people died unnecessarily because of multiple government failures during the Covid-19 crisis.

Meanwhile, Hancock revealed the Delta variant of coronavirus first identified in India now represents 91 per cent of all new cases in the UK. Amid rising hospital admissions, the UK on Thursday recorded 7,393 new cases.

Cummings, who quit as Johnson’s chief adviser in November, claimed during a joint hearing of the Commons health and science committees last month that he had repeatedly urged Johnson to sack Hancock because of “15 or 20 things”, including his “lying”.

Cummings said Hancock lied to Johnson about people being tested for Covid-19 before being moved from hospitals to care homes. It only happened sporadically in the early weeks of the pandemic.

Care homes account for about 42,000 of the 127,000 deaths recorded in the UK from Covid-19 so far. Cummings has described the government’s repeated claim to have put a protective “shield” around care homes as “nonsense”, saying the opposite was true.

In his testimony to MPs, Hancock said his promise to the prime minister was that people being moved from hospital to care homes would be tested if and when sufficient capacity was built up.

He admitted many people were transferred without testing but said he had acted on the advice of experts. “On care home policy throughout we followed the clinical advice,” he said.

Barbara Keeley, a Labour MP, told Hancock that care operators had “repeatedly warned” in March 2020 about the dangers of discharging old people into care homes without testing and chastised the government for not taking account of the sector’s views.

“Given the terrible excess mortality . . . do you recognise that this failure to include expertise from the care sector was a mistake?” she said.

Hancock said the government had been moving “at remarkable speed” without the ability to undertake the usual full public consultation. He also said the mortality rate in care homes “weighs heavily” on him.

The health secretary earlier admitted that the government did not have a full list of all care homes in the country at the start of the crisis.

He also said infections in care homes came largely from staff and other “community” sources, citing estimates from Public Health England.

But Greg Clark, Conservative chair of the science committee, challenged that claim. “Isn’t it a stretch of the imagination to believe that [a small proportion of infections] are attributable to hospital transmission into care homes, when we simply don’t have the data?” he asked.

Hancock said the PHE estimates were “the best assessment that can be made given the facts on the ground . . . It’s always a challenge to measure these things.”

Responding to Cummings’ allegations, Hancock denied ever telling an untruth, saying he had acted with “honesty and integrity” throughout the crisis.

He said he had no idea why Cummings held him in such low regard. “The best thing to say is that government has operated much better over the last six months [since Cummings left].”

The health secretary said he could “face the mirror each morning” as he did everything he could to save as many lives as possible during the pandemic.

He defended his record on procuring supplies of personal protective equipment for health workers, saying there was never a “national shortage”.

He denied that any worker died because of a lack of gloves, masks or gowns, saying: “We’ve looked into this and there’s no evidence that I have seen that a shortage of PPE provision led to anybody dying from Covid.”