"We understand this is very frustrating for customers on these two cancelled flights and we've apologised to customers.
"We are putting customers on other flights and will get them to their destination as quickly as possible," the spokesman said.
Passengers had been offered refunds, offered flights for later today or on Monday or re-routed via Christchurch.
However Aucklander Dinithi Seneviratne said the two other flights for Sunday were booked out within minutes of being notified her 1.35pm flight had been cancelled and she was told by the call centre a refund would take 15 working days to process.
She said she received a "parrot-like apology" from a call centre worker who said they could not do anything.
So instead her and her daughter have had to shorten their trip to Wellington and will fly out on Monday morning instead.
Seneviratne had also looked at flying Air New Zealand but said there were no flights available.
"It was really abrupt. Just we are sorry - there is a crewing error. We don't have enough crew to fly and so you will just have to deal with it."
Angrez Singh told the Herald he had been due to fly from Auckland to Wellington at 1.35pm, which was one of the flights cancelled last night. After being told there were no flights available today, Singh booked a flight with Air New Zealand which cost him another $100.
While Lisa Hill and her mother Yvonne Smith said their fun weekend at the World Of Wearable Art Show had been ruined by having their flights cancelled.
Hill was on the phone with Jetstar until midnight on Saturday night trying to work out how to get a connecting flight to Kerikeri which was where her car was parked.
After missing out on a flight on Monday morning she felt pressured to take one later in the day without checking whether she could still get an Air New Zealand flight to Kerikeri and when she found out she couldn't Jetstar refused to refund her.
She instead ended up paying an extra $331 for new flights flying Air New Zealand tomorrow as well as her existing Jetstar fare and hotel cost.
She said the experience was extremely frustrating and felt Jetstar was unsympathetic about the situation it had put her in.
Jetstar has said it would pay for accommodation for up to $150 for passengers who could not fly until tomorrow and did not live in the city they were stranded in.
Passengers were notified by text and email last night at about 9.30pm.
Cancelled flights
JQ262 WLG to AKL 6.20pm - 7.25pm
JQ263 AKL to WLG 4.45pm - 5.50pm
JQ258 WLG to AKL 3.10pm - 4.15pm
JQ259 AKL to WLG 1.35pm - 2.40pm