The airline said the shake-up would bring “more low fares and more local jobs” to those two countries.
But more than 500 Jetstar Asia staff would lose their jobs.
The company said affected employees would be offered redundancy payouts, and where possible, new jobs elsewhere with Qantas or in the aviation sector.
“Only 16 intra-Asia routes will be impacted by the closure of Jetstar Asia, with no changes to Jetstar Airways and Jetstar Japan services into Asia,” Qantas said today.
“All of Jetstar Airways international services in and out of Australia remain unchanged.”
Jetstar Asia’s website said the airline’s inaugural flight took off for Hong Kong in December 2004.
But Qantas said the operator had faced rising supplier costs, high airport fees and intense competition.
Jestar Asia’s last day of operation will be July 31 this year.
Qantas said customers with bookings on cancelled flights would be offered full refunds or be given seats on other airlines if possible.
John Weekes is a business journalist covering aviation and court. He has previously covered consumer affairs, crime, politics and court.