Flight JQ279, an Airbus A320 carrying a near-capacity 177 passengers, landed at 12.20pm.
It had been due to arrive at 10.50am.
The airline's commercial executive manager, David Koczkar, said four new airports and 18 flights on the same day was a "large operational launch" and apologised for delays and inconvenience.
Robyn and Graham Haywood, of Auckland, said while they could not complain about the cheap ticket price ($206 return total), their Jetstar experience had been a "comedy of errors", starting with a take-off delay of about an hour, then further delays on the tarmac, in the air when the plane was forced to wait for congestion to clear - and on the Queenstown airfield.
Another blow for the low-cost Qantas subsidiary on its first day of operations in New Zealand came with rival Pacific Blue's 10am announcement it will add new direct services to Australia from Queenstown, Dunedin and Wellington from September 1.
When asked by the Otago Daily Times if Jetstar would introduce a Dunedin link, Mr Koczkar said: "The customer will decide and will demand services to different destinations, or demand growth in existing destinations.
"If we're strongly patronised on services to Queenstown, we will look at adding more services."
The carrier would gauge demand for a Dunedin service by discussions with the airport, Tourism Dunedin and Tourism New Zealand.
Mr Koczkar said "several" short-haul Airbus A320s would be arriving between June this year and June 2010, across the entire Jetstar network.
Another increase across the network was planned for the following two to three years.
When asked what Pacific Blue competition would mean for customers, Mr Koczkar said when customers booked on Jetstar at a similar date and time, the airline would beat any competitor by 10%.
Queenstown Airport chief executive Steve Pahl said Jetstar would take over from Qantas on domestic gates 2, 3 and 4, but Qantas would continue its international flights.
"Pacific Blue are going to fly two Sydney flights a week, on Tuesdays and Saturdays. I think it goes to show Queenstown is an attractive destination for Australians."
Destination Queenstown chief executive Steve Sanderson said Australians made up 45% of tourists in the resort.
The organisation was devoting half of its $3 million budget to the Australian market over the next year.
"Certainly, we're seeing continued strong demand for Queenstown. If airfares are going to be competitive, that's a good thing for the industry."
