Of the planned passenger group, 72 were banned from the flight home to Australia after 48 tested positive for coronavirus.
The other 24 were family members of positive cases and deemed close contacts.
The first repatriation flight is due to leave New Delhi after the ban on returned travellers was lifted today.
The positive diagnoses mean they will be stuck in India until they recover.
The Department of Foreign Affairs and Trade are working to fill the flight with more passengers but the obstacle of 48-hour pre-flight testing will make this difficult.
The plane has departed Darwin, bringing valuable medical supplies to India, and is set to return to Australia tomorrow with the passengers who have been allowed to board.
They are due to spend quarantine at a facility in Howard Springs in the Northern Territory.