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Jetstar's best performing route during the week was between Nelson and Wellington with 54.8 per cent of flights on time, according to the figures Air New Zealand said had been supplied by an "independent company."
In the last week of January on the Auckland-Nelson and Auckland-Napier routes, Jetstar was running at 43 per cent.
But a Jetstar spokesman said regional on-time performance had been steadily improving since the airline launched services on December 1 last year.
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While the airline didn't respond directly to the figures supplied to Air NZ, during January Jetstar said its regional on-time performance was 70 percent, with a number of days over 90 percent and some at 100 percent.
In February the airline introduced three new regional routes serving Palmerston North, New Plymouth and Wellington in addition to services between Nelson, Napier and Auckland.
With those new routes it had more than doubled the number of weekly regional flights from 80 to over 220.
"This is a significant expansion and naturally these new routes and additional services need time to become established," the Jetstar spokesman said.
In New Zealand, airlines gather their own on-time performance data and this has sparked arguments between them in the past.
Jetstar flies five 50-seat Bombardier Q300s on regional routes and says it has sold tens of thousands of regional tickets under $50 since it went on sale last August.
Air New Zealand is also increasing capacity and dropping prices in the regions.
Napier, now served by both airlines, is enjoying a passenger boom with Hawkes Bay Airport saying passenger numbers were up 13.5 per cent for the first six months of the financial year and numbers for the year forecast to exceed 500,000 for the first time.