Australian citizens could face up to AU$66,000 in fines and up to five years in jail if they try to return home during the temporary travel ban.
Federal Health Minister Greg Hunt confirmed the temporary pause on travellers from India, including Australian residents, will be effective on Monday.
It comes as the country continues to experience the worst surge in COVID-19 cases since the pandemic began, reporting more than 300,000 new cases daily for nine days in a row.
Hunt says anyone who tries to breach the travel ban, including travelling via other countries such as Singapore of the United Arab Emirates, will be charged.
"Failure to comply with an emergency determination under the Biosecurity Act 2015 may incur a civil penalty of 300 penalty units, five years' imprisonment, or both," Hunt said on Saturday.
"The Government does not make these decisions lightly. However, it is critical the integrity of the Australian public health and quarantine systems is protected and the number of COVID-19 cases in quarantine facilities is reduced to a manageable level."
The temporary pause will be reviewed on May 15 following advice from the Chief Medical Officer.
Melbourne GP and health commentator Vyom Sharma said the move is "incredibly disproportionate" to the threat posed by returning Australian citizens.
Dr Sharma told ABC's Weekend Breakfast he's "concerned" the government is "so sensitive" to the risk, they can't take the increased load of people coming in.
"Why is it that their first instinct is to stop flights, stop people from coming in, abandon them to a country where literally oxygen is running out, and not having proven infection and prevention control in quarantine in the first place?"
He questions whether it's "consistent" with other countries in the past.
"What strikes me as also bizarre is that the USA back in January was returning to us Australians in much higher quantities of people who were testing positive, and yet there was no talk of plan banning those flights then."
Australia to provide emergency medical supplies
The Australian government has agreed to provide emergency medical supplies, including 1000 non-invasive ventilators.
One million surgical masks, 500,000 P2/N95 masks, 100,000 surgical gowns, 100,000 goggles, 100,000 pairs of gloves and 20,000 face shields will also be provided.