As the country looks set to surpass a 90 per cent first-dose rate as soon as Saturday, the prime minister said he respected a person's right to choose, should they not want to get the vaccine.
"We live in a country where we are not going to go around demonising those who want to make their own choices," Mr Morrison told the Seven Network on Thursday.
"Of course we want people to get vaccinated but we are not going to take that heavy-handed approach."
The comments were made after former NSW premier Bob Carr on Twitter called for anti-vaxxers to be stripped of their Medicare reimbursements, should they later contract the virus and be treated in hospital.
Several states such as NSW and Victoria have mandated vaccines for entry to services such as retail and hospitality.
Queensland has also introduced plans to exclude unvaccinated people from venues when the state reaches 80 per cent fully vaccinated.
The prime minister said immunisation rates continue to grow at a rapid pace.
"NSW is now 90 per cent double-dose, Victoria will soon be there and we have other states that have had less COVID now 80 per cent (have had) ... their first dose," Mr Morrison said.
"We will hit 90 per cent first dose this weekend for the whole country and we got there because we trusted Australians."
On Thursday, NSW reported 261 new local cases and one death while Victoria reported 1313 new infections and four fatalities.
Meanwhile, 82 per cent of the national population over 16 are fully vaccinated.
It comes as Australia's medical regulator granted a provisional determination to Moderna for its vaccine for children between six and 11.
Currently, the Moderna vaccine is eligible only for people 12 and over.
The Therapeutic Goods Administration is also examining data from manufacturer Pfizer to approve its vaccine for children.
US regulators have already approved the jab for children.