The prime minister rejected the assertion the country was left underprepared for worst case scenarios despite extensive modelling on various possibilities by the health department.
"I don't accept the suggestion that they haven't been doing their job. I think they've been doing their job extremely well and under extraordinary pressure in a very uncertain environment," he told reporters on Thursday.
But criticism continues over the availability and affordability of RATs after changes to Australia's testing regime announced after Wednesday's national cabinet.
People who test positive on a RAT don't have to get their results confirmed with a PCR test in the hopes of easing pressure on overwhelmed clinics.
But University of Melbourne epidemiologist Professor Tony Blakely warned surveillance would not be accurate going forward with the tests mainly being done at home.
"The horse has bolted, this is the biggest policy failure so far in Australia," he told the Seven Network on Thursday.
"We also haven't thought about how you can load up that data to the surveillance system, so we won't get that in place in the next couple of weeks."
But Mr Morrison said it was more important to connect people with care than reporting numbers.
"Case numbers are less of an issue (and) will be underestimated in Australia because we know that people are self managing in many instances," he said.
"What matters first is that people who have COVID (is) the care they get connected to."
Mr Morrison noted national cabinet is working through how to more accurately record case numbers so hospitals were able to prepare.
Infectious disease expert Professor Peter Collignon said getting a PCR confirmation of a positive rapid test doesn't add much, telling people to stay home and isolate if they have a positive test.
"If you're vaccinated and are a 30- to 40-year-old, your chance of coming into grief is really low. We have support if you need it but don't get on the (PCR) queue and delay the older people who may need to be in front of you," he told Sky News.
It comes as NSW registered another 34,994 new cases on Thursday and a further six deaths.
There are 1609 patients in hospital, with 131 in intensive care.
Victoria recorded a new one-day high for new cases, with 21,997 infections and six deaths.
The state has 631 patients in hospital with 51 in intensive care and 22 of those on ventilation.
There were a record 222,565 booster shots delivered on Wednesday.
Mr Morrison said 200 million rapid tests would be available in coming weeks but ruled out making them universally free, instead providing 10 tests over a three-month period to concession cardholders, which covers more than six million people.
Labor senator and chair of a parliamentary COVID-19 committee Katy Gallagher hit out at the concession plan, saying the Australian pandemic response had been one where everyone was in it together.
"Huge amounts of funding has been provided to ensure we have been able to live safely. Providing rapid antigen tests to everybody is part of that approach," she told Sky News.
Health Minister Greg Hunt said tests have always been free for health purposes.
"When you go to a testing clinic, whether it's a PCR test or a rapid antigen test, and you are going for symptoms or as a close contact, that remains the case that is free," he told the Nine Network.
"If you are using them for somebody coming to your house or other social or casual uses, then there is an additional private market where people can access that."
