Prime Minister Scott Morrison says he is “deeply sorry” for failures in the aged care sector during the coronavirus crisis, but has defended the government’s overall response.

It comes amid ongoing tension between the Health Department and the Royal Commission into Aged Care Quality and Safety, which this week heard many of the deaths in aged care homes were preventable.

Some statements made to the commission have been hotly contested by senior health officials, but Mr Morrison said he acknowledged that on “some days” the pandemic got the better of the government’s response.

“On the days that the system falls short, on the days that expectations are not met, I’m deeply sorry about that, of course I am,” he said.

“I know that everyone who is involved in the process who is trying to meet those expectations is equally sorry.

“On days where workforces are completely stripped from facilities and there is nobody there, and you scramble for a workforce to try to put them in place, and you have ADF officers who go there at 11.00 at night to try to clean up the mess, that’s not good enough.”

But Mr Morrison backed health officials who disputed several statements made in the royal commission this week.

Earlier on Friday, the head of the Health Department, Professor Brendan Murphy, accused the aged care royal commission’s lawyer of using misleading statistics to criticise the government’s response to COVID-19.

Professor Murphy disputed some of the aged-care claims when he appeared before the inquiry on Friday. Photo: AAP

Professor Murphy, who was Australia’s chief medical officer until June, and other members of the federal health bureaucracy have bristled against evidence presented in the commission this week.

Several times during this week’s hearings, counsel assisting Peter Rozen QC said aged care was overrepresented in Australia’s death toll.

“Presently, 68 per cent of all COVID-19 deaths in Australia relate to people in residential aged care,” he said in his opening remarks on Monday.

“The evidence that you will hear is that this makes Australia the country with one of the highest rates in the world of residential aged care deaths as a proportion of deaths from COVID-19.”

• ‘Unforgiveable’: Aged care still ‘not properly prepared’ for virus

By his closing statement on Thursday, he said that proportion had increased to 70 per cent.

On Friday, Professor Murphy told a Senate committee that using those figures to suggest Australia was performing poorly was an “extraordinary interpretation of statistics”, labelling the conclusion “ludicrous”.

“When you have a very, very low death rate generally, then the aged care death rate as a proportion is high,” he said.

“Every death is an absolute tragedy and it’s been an awful situation, but to interpret a percentage of an extremely low death rate as an example of poor aged care management is simply not defensible.

“I don’t believe any expert … would agree with that as a conclusion, we find that a very misleading conclusion.

“We’ve had tragic deaths in aged care, but it is only 0.1 per cent of aged care residents, compared to 5 per cent in the UK. Other countries have had 20,000 deaths.”

Ambulances and medical staff at the coronavirus-hit St Basil’s aged-care home.

The committee’s chair, Labor senator Katy Gallagher, said: “Do you think for the families of those that have lost loved ones that that statistic would be particularly difficult to accept?”

Professor Murphy responded that the government viewed every death as a tragedy.

Outside the committee, Mr Morrison also disputed assertions made by Mr Rozen that there was no specific plan for the aged-care sector to deal with COVID-19.

“The government has provided its response to those assertions and the government maintains very strongly that the plan was in place,” he said.

“There has been a plan and it has been updated, and so we completely reject the assertion that there was not a plan.”

In his closing submission on Thursday, Mr Rozen told the Royal Commission into Aged Care Quality and Safety that: “Based on the evidence that you’ve heard, the sector is not properly prepared now.”

“Tragically, not all that could be done was done.”

But Professor Murphy told the committee he disagreed with that assessment.

“Respectfully, I would disagree with counsel assisting,” he said.

“I reject the assumption that we haven’t done a huge amount of work in preparing the sector in a range of areas.”

Asked by Labor senator Kristina Keneally whether he accepted any of the criticisms levelled against the government in the royal commission, Professor Murphy conceded the workforce could have been better prepared.

“I don’t think anyone expected that several thousand health workers – our health and aged-care workforce is the same workforce – would be in quarantine and isolation, and we would have such a critical issue in health workforce,” he said.

“We’ve never seen that anywhere else in the country.”

He said he would reflect upon statements made in the commission, and its findings, before providing a more detailed answer.

-ABC