The announcement follows Emirates' decision earlier this year to cease its service between Auckland and Sydney.
The Oneworld carrier says it will add new daily return services on the Melbourne-Auckland route, and an additional two weekly services between Brisbane and Auckland.
Emirates, which operates the world's largest wide-bodied fleet, now flies its flagship Airbus A380 superjumbos daily from Melbourne and Brisbane to Auckland and back, and the international-grade business class seats and first class suites have proven popular with business travellers. The immediate effect is estimated to be about 300,000 fewer seats per year, out of about 10.2 million total, and from March 2018, flights between Australia and New Zealand might get more expensive.
Following the latest changes, FlightGlobal schedules show that Emirates' only transtasman flight will be its daily Sydney-Christchurch services, which are operated by A380s.
Air New Zealand Ltd, the biggest flight operator between the two countries, is likely to benefit the most from the capacity cut, which could boost airfares.
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The new agreement, which needs to be signed off by the Australian Competition and Consumer Commission, includes a recently-announced major overhaul of routes that were part of the initial five-year Qantas-Emirates partnership agreement.
Qantas has said its new trans-Tasman flights will be connecting seamlessly to its London services.
"Reauthorisation of the partnership will allow us to leverage our combined network strengths", Emirates airlines president Sir Tim Cook said.
Emirates is evaluating the possibility of adding another non-stop Dubai-Auckland flight or a new non-stop Dubai-Christchurch flight in the future, Clark said. "It will enable us to continue developing world-class customer experiences, and contribute to stimulating increased opportunities for global trade, tourism and commerce".
Qantas chief executive Alan Joyce said the changes reflected "customer demand, new aircraft technology and our respective network strengths".
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According to the airlines, since 2013 more than 8 million passengers have travelled on the joint network, travelling more than 65 billion kilometres.
"It's been a very successful sponsorship for us over many years", he said.
Qantas and Emirates plan to increase their direct services to New Zealand.
The changes will "enable Emirates to reschedule its Australia flights to create a better spread of departure times throughout the day", the statement said.
The airlines began working together in 2013 to share revenue and passengers flying from Australia to Europe through Emirates' Dubai hub.
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Centre for Aviation (CAPA) commentary ahead of the August news, said Qantas had the upper hand in the partnership, but that it was worthwhile for Emirates to maintain the deal to avoid the risk of Qantas teaming up with an Emirates competitor.