Mr Morrison said the jump in infection rates from India across all Australian quarantine hotels had jumped from 10 per cent to 50 per cent in recent weeks.
Mr Morrison said his government had faced the same accusations it was racist when it stopped flights from mainland China at the beginning of the pandemic.
“That was one of the most important decisions we made as a government,” Mr Morrison said.
“There is a raging pandemic (in India) and we need to just continue to take decisions that are in the best health interests of Australia.”
Mr Morrison said the “more virulent strains” circulating in India could devastate Australia.
“This is a temporary arrangement,” he said, “it has been put in place to ensure that we do not get a third wave here in Australia.”
Mr Morrison said the blanket travel ban which allows the government to send Australians to jail if they try to fly home would be used “very, very carefully”.
Changes to the Biosecurity Act mean Australians could face up to five years in jail and heavy fines if they flee India and try to enter Australia.
The changes in the Biosecurity Act had been active for a year, Mr Morrison said, adding that in that time “no one’s going to jail, there hasn’t been any irresponsible use of those powers.”
“I understand the measures have strong sanctions,” he said.
He said Australians can be assured the law would be used “appropriately and responsibly”.
Australia had avoided 30,000 coronavirus deaths because of sometimes “unpopular” decisions he has had to make, Mr Morrison said.
The average fatality rate experienced by other OECD countries would have caused tens of thousands of deaths in Australia, he claimed.
“We prevented that here in Australia by working together, but it’s also meant we’ve had to take some unpopular decisions on occasions.”
To assist with the India health crisis, Australia was sending 1000 non-invasive ventilators, one million surgical masks and 100 oxygen concentrators.
While the flight ban is scheduled to last until the middle of May, Mr Morrison is meeting with Health Minister Greg Hunt and the national chief health officer on a weekly basis to gauge lifting the block early.
“I want to ensure that we ready our facilities and our systems and our testing arrangements … to ensure we can bring more Indian-Australians home,” he said.
Mr Morrison said he was eager to get repatriation flights back up and running as soon as possible.
There are believed to be almost 9000 Australians in India wanting to return home.