It was scheduled to take off at 11.10am but instead left at 12.35pm - arriving an hour and 25 minutes late.
A Jetstar spokesman said their regional network on-time performance was over 88 per cent for departures and 87 per cent for arrivals in August.
"Our performance in Hawke's Bay is in line with this overall network result."
MetService Meteorologist Angus Hines said the strongest gusts recorded at the airport were between 9am and 11am.
Gusts of 80km/h were recorded and the strongest mean speed and average speed was 55km/h.
Today's events are part of a string of delays relating to weather and control tower issues.
Last week, heavy fog forced the cancellation of 16 flights, including Jetstar ones.
Several flights into the Napier-based airport had to be abandoned with some aircraft unable to land in thick fog, while flights out of the airport had to be cancelled before take-off.
Also on Tuesday, NZ5883 service from Napier to Wellington was delayed by 10 minutes while "pilots carried out additional pre-departure processes as the aerodrome was under air traffic control contingency procedures", the airline said at the time.
The previous week, Minister of Police and Napier MP Stuart Nash complained on Twitter when his flight was delayed due to a air traffic controller running late for work.