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The airline said it was unable to continue its operations in New Zealand while there is a requirement to keep the middle seat free.
"The limitations on the number of customers that are allowed on board our aircraft make the operations of our flights unviable," Jetstar said.
Customers will be contacted and will be able to reschedule their flight or receive a credit voucher.
"As per our Fly Well programme, we have implemented a range of measures to ensure safe air travel.
"These include initiatives at airports and on board, like encouraging online check-in, providing every customer with a kit that has a mask and sanitising wipes. We carry spare kits on board in case someone needs to change their mask during the flight," the airline said.