Air New Zealand flies up to five times a week at peak season but the arrival of Emirates' daily service using a 777-300ER aircraft added close to 130,000 seats across first class, business class and economy all year on the route.
Emirates also uses Bali as a lure to travellers flying on to Dubai and beyond (and inbound tourists to New Zealand from the Northern Hemisphere) after axing some Airbus A380 services.
Bali has surged in popularity this year.
Travel by Kiwis to Bali was up last month to more than 10,200 - up by 55 per cent on August last year.
Last year 40,000 New Zealanders flew to the Indonesian island.
Passenger booked on the cancelled Emirates flights will be rebooked on alternate flights.
''Emirates apologises to our customers for the inconvenience caused.''
Passengers with bookings on the affected flights should contact Emirates or the travel company where their original booking was made for help, the airline said.
''Our Auckland-Bali route remains an important business and leisure destination for Emirates and we remain committed to serving our customers in both Auckland and Bali,'' said a spokeswoman.
Emirates axed its Auckland-Melbourne and Auckland-Brisbane Airbus A380 superjumbo services in March. It still flies daily with an A380 from Auckland to Dubai and to the Middle Eastern hub from Christchurch via Australia.
At the weekend flights to Bali via Australia on Virgin Australia were offered for $599.