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The woman, who does not want to be named, said she, her sister and two nieces were about to board a flight home on December 11 when staff informed them their carry-on luggage, including the cherries, was overweight.
"They took them off us and said they would dispose of them the next day."
Staff did not give them the option to lighten the weight by taking some cherries out of the box as the flight was boarding and they were told there was no time.
They also refused an offer to pay for excess baggage as they did not accept cash, she said.
The woman said she and her family members had picked the fruit at Cheeki Cherries near Cromwell and she contacted owner Martin Milne after arriving back in Auckland to see if there was another way to get them sent to her.
It was Mr Milne who discovered half the box had been eaten when he went to the airport the following day.
Mr Milne said he happened to be near Queenstown and decided to call in at the airport.
He said he dealt with a man he believed was a baggage handler.
"It was Saturday and there was hardly anyone around but this young guy was very obliging.
"He said ‘yeah I think I saw a box of cherries in the fridge’."
When he brought them out the truth was revealed.
"Sure enough it was a half-eaten box of cherries."
Mr Milne said he otherwise would have boxed the cherries and sent them to Auckland by courier on the following Monday.
"To me, it is like they basically took her luggage and stole it."
The woman said the fact the cherries had been eaten was insulting.
"They’ve got no right to eat them. It is against their policies.
"We picked those cherries with love and that is what hurt."
Her sister had been offered $50 compensation but that was little comfort, she said.
A Jetstar spokesman said it appeared there had been a breach in protocol and the company was investigating.