However, Immigration NZ and Jetstar confirmed they had customers debited multiple times between Tuesday and Friday last week.
The error has been resolved and MasterCard is processing refunds.
An Englishman based in Auckland, who asked not to be named, told the Herald the glitch caused him significant stress on Friday as he was unsure how he would buy food and nappies for his 15-month-old son over the weekend.
The truck driver applied for a $1250 Partnership Resident Visa through Immigration NZ. He was debited for it twice on Friday morning, which put his account into overdraft.
"It was nightmare. I didn't know how we were going to survive the weekend.
"I had to call the bank to get an emergency overdraft for the weekend and my car insurance was due but that didn't go through because of the overdraft so I had to call them and explain what had happened.
"I spent all day on the phone to Immigration NZ . . . When you live week-by-week, you notice when an extra $1250 goes missing from your account."
The man said he told Immigration NZ he had a young son to look after, but was given no advice on how he could meet his costs.
He was eventually told on Friday evening he would be paid back on Saturday morning. The repayment came through on Saturday afternoon.
Immigration NZ area manager Darren Calder said it apologised to customers for the distress the duplicate payments caused.
He said it hadn't been confirmed how many customers were affected, but it was believed to only be a small number.
A Jetstar spokesman said Jetstar regretted the inconvenience the issue had caused customers. He wouldn't divulge how many customers were affected
