Massive fines or up to five years behind bars are in place for people who find a way around a temporary pause on travellers from India.
The government has copped strident criticism from doctors, human rights groups and the Indian-Australian community over the punitive measures.
The prime minister insists the measures are not racist.
"It's being put in place to ensure we do not get a third wave here in Australia and that our quarantine system can remain strong," Mr Morrison told 2GB radio on Monday.
"I understand the measures have strong sanctions with them but we've had the Biosecurity Act in place for over a year and no one's gone to jail."
He is adamant the powers will not be used irresponsibly.
While Mr Morrison and senior ministers have pointed to health advice as the basis of the decision, Chief Medical Officer Paul Kelly said the powers already existed.
"There was no advice given in relation to the fines or jail terms, that's just how the Biosecurity Act works," he told ABC radio on Monday.
"Our advice was that we needed to do something about the number of positive cases coming into our hotel quarantine because of the risk of incursions."
There are about 9000 Australians in India who want to return home, with 650 considered vulnerable.
Australian Medical Association WA president Andrew Miller said similar measures were not in place for people in Europe or the UK during serious coronavirus outbreaks.
Dr Miller said it would be viewed as a dark period in the nation's history.
"It's not Australian to trap people overseas," he told the Nine Network.
"To suggest that a particular segment of the community should get fined for this is absolutely unacceptable and outrageous."
He apologised to Indian-Australians that he wasn't able to do more to stop the imprisonment and fine powers being used.
Mr Morrison said it was a temporary arrangement in place while quarantine and testing are strengthened.
"I want to get those repatriation flights running safely again. These are the things I have to do to ensure we can do that."
Yadu Singh, a Sydney cardiologist and president of the Federation of Indian Associations of NSW, said the government had a moral obligation to help its citizens.
"There is a panic. There is a worry because coronavirus is a big, big problem in India and these people are stranded," he told ABC radio.
India is recording about 400,000 new coronavirus cases each day but the real number of people contracting it is believed to be higher.
The Australian Human Rights Commission wants the government to prove that its decision to fine or jail Australians is not discriminatory.