The first flight will depart from the Peruvian city of Cusco for Chile’s capital Santiago before travelling on to Melbourne.
A second journey will start in Peru’s capital Lima and stop in Iquitos en route to Melbourne.
Demand is expected to outstrip the number of seats available after more than 400 Australians registered with the consulate to get on the next plane home.
Foreign Minister Marise Payne has signalled another flight would be arranged in coming days.
“Australians in Peru will be able to book for an Australian government-facilitated commercial flight to Australia this Wednesday out of Lima, Cusco & Iquitos,” she posted a tweet on April 6.
Australia’s ambassador to Peru and Bolivia Diana Nelson said she was delighted to confirm the flights.
“Working hard to get you home,” she said in her tweet.
Sydney man Thomas Curnow is among hundreds of people hoping to get on one of the flights.
“It’s 11 p.m. now and I’m filling out details and stuff for the flight,” he told AAP from Peru.
In an email to Australians in Peru, the consulate said a seat would cost $1,539 (AUD $2550) a person.
Australian tourists in Cusco and Iquitos will be given priority, along with vulnerable travellers, the elderly and families with children.
Those not in priority groups will be placed on a waiting list.
“We ... expect this flight will be oversubscribed, and encourage Australians who wish to return to Australia to book as soon as possible,” the consulate’s email reads.
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