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Up to 1.7 million travellers who previously didn't need a visa now have to use an Electronic Travel Authority (ETA).
The government confirmed unofficial websites were charging up to 10 times the processing fee for the mandatory ETA.
Travellers can request one online for $12 or through an app for $9.
Mondumo Small Group Tours director Colin Mairs said some clients were confused by the new process, and had been caught out.
"Two days ago a lady contacted me, she's already in Australia and in a bit of a panic because she thought she'd applied for her NZ ETA," Mr Mairs said.
"Speaking to other travellers there realised she didn't get any confirmation email. It looks like she probably applied through one of the fake websites. She's been scammed so I advised her to apply again and make sure you've got it."
While the ETA has caused stress for some travellers, Mr Mairs said it was a good process to have, even if it took a bit of time to get used to.
Tourism Industry Aotearoa chief executive Chris Roberts said some of the false websites looked more official than the government site.
"These fake sites are a fact of life. Other countries haven't been able to get rid of them. We have to our very best to let would-be travellers know that there is only one official site and there is only one price - $12, and if you're paying more than that, you're on the wrong website and don't waste your money," Mr Roberts said.
Some of the funding from the electronic travel authority's $5 million PR campaign should be earmarked to warning people against these scam websites, he said.
Board of Airline Representatives NZ executive director Justin Tighe-Umbers said the scam was creating unpleasant experiences for some travellers.
"Obviously it's really disappointing that's there's a criminal element who are choosing to use this as an opportunity to target unsuspecting travellers," Mr Tighe-Umbers said.
While he could not confirm the number of people affected, he said more than 85 percent of passengers arrived at an airport with the right ETA.
Tourism Export Council chief executive Judy Chen said any visitors facing higher fees needed to double check they were on a legitimate site before proceeding.
"We really just have to keep continuing our messaging to our visitors that there are fake sites out there and to be really vigilant when people are jumping on the internet," Ms Chen said.
Some examples of unofficial third party visa websites include: