The budget airline announced flights between Darwin and Denpasar in Bali are cancelled from October 9 to October 28 due to runway works at the city's airport.
"We have received confirmation from the Department of Defence that Darwin Airport runway works are going ahead in October," the airline said in a statement.
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"We are contacting customers who are booked to travel during the three-week works period to discuss their options including indirect flights via another port, a travel credit, or a refund to their original form of payment."
Jetstar said it understands this will be "disappointing and frustrating" for impacted travellers.
"We thank them for their understanding," the airline said.
The airline added it "proactively" stopped taking bookings for flights between Darwin and Bali during this period to limit the number of customers impacted while it waited for confirmation the maintenance would go ahead.
"We look forward to resuming our flights from Darwin to Denpasar from Sunday 29 October 2023," Jetstar said.
Jetstar flights are still available from other cities to Bali during this period.