From Monday, any Australian arriving in the country from India faces fines and up to five years in prison.
It comes after Canberra banned all flights from the virus hotspot until 15 May.
Prime Minister Scott Morrison has dismissed accusations of racism.
"The same accusations were made against the government over a year ago when we closed the borders to mainland China," he told Sydney radio station 2GB.
"There's no politics or ideology in a pandemic... It's got nothing to do with politics, this is a virus."