"All I simply did yesterday was draw attention to some basic facts that I think are well understood by all Australians and particularly by all Victorians," he told reporters in Canberra on Wednesday.
"I wasn't seeking to direct any blame anywhere. I was just basically calling out what was the simple facts.
"We can't ignore the fact of what's happened in Victoria and I don't believe the Victorian premier is ignoring it either. That's why we're working together to deal with the consequences of what has occurred in Victoria."
Mr Morrison has also raised concerns directly with the Victorian premier about his push to extend emergency powers to enforce health orders for a further 12 months.
"I think it's important to dispel any uncertainty and get clarity around that issue," the prime minister said.
"I think people are concerned the lockdowns will extend for another 12 months.
"Of course, I don't think that's what the premier was suggesting at all but in these times we've got to be very careful about the announcements that are made and I welcome the fact that he was clarifying that yesterday."
Victoria has suffered a sharp rise in coronavirus deaths, with 24 fatalities recorded on Wednesday, taking the national toll to 549.
The state recorded another 149 infections, with new cases below 150 for the third consecutive day.
The NSW government has moved 366 people out of a Sydney hotel after dumping it from the quarantine program over health standards.
NSW and South Australia are weighing up easing restrictions on borders with Victoria after pressure from industry and the federal government.
Australian health authorities are concerned about the first documented case of coronavirus reinfection after a Hong Kong man caught the disease twice.
The 33-year-old was cleared of the virus and discharged from a hospital in April but tested positive again after returning from Spain via Britain on August 15.
The findings about the man indicate the disease, which has killed more than 800,000 people worldwide, may continue to spread despite herd immunity.
Australia's chief nurse Alison McMillan confirmed the expert panel dealing with the pandemic was monitoring the research.
"This is obviously something we are concerned about but this is the first reported case," she told reporters in Canberra.
"We will continue to monitor the evidence as it grows and consider this in relation to our response."
Metropolitan Melbourne residents are subject to Stage 4 restrictions and must comply with a curfew between the hours of 8pm and 5am. During the curfew, people in Melbourne can only leave their house for work, and essential health, care or safety reasons.
Between 5am and 8pm, people in Melbourne can leave the home for exercise, to shop for necessary goods and services, for work, for health care, or to care for a sick or elderly relative.
All Victorians must wear a face covering when they leave home, no matter where they live.
People in Australia must stay at least 1.5 metres away from others. Check your state’s restrictions on gathering limits.
If you are experiencing cold or flu symptoms, stay home and arrange a test by calling your doctor or contact the Coronavirus Health Information Hotline on 1800 020 080.
News and information is available in 63 languages at https://sbs.com.au/coronavirus