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The agency last month issued a media release urging tourists to use official apps or websites to apply for the new online visa and international levy.
The levy came into effect on July 1 requiring many tourists, working holiday visitors, some workers and students to pay $35 each to help fund tourism infrastructure and conservation projects.
However, unofficial foreign websites began popping up, with some charging astronomical fees to would-be visitors.
Since the NZeTA became mandatory, about 300,000 have been processed and more than 100 requests refused.
Aldous said INZ would not be able to assist travellers who had concerns about the validity of NZeTAs purchased from unofficial sites because the transaction "is between the traveller and the site they used".
"Most are legitimate sites that charge a fee to provide a service, but a small proportion of these are fraudulent sites," Aldous said.
"INZ continues to undertake extensive communication activities to inform travellers how to apply for their NZeTA using the official INZ website or mobile applications."
These, Aldous said, include specific warnings and raising awareness of these sites.
"Travellers shouldn't need to fork out more money than the official cost and should make sure that they aren't being misled into paying more," Aldous added.
INZ general manager Stephen Dunstan said some third-party sites claimed to be able to provide an expedited service, but there was no such thing.
In some cases, he said, third parties were also collecting additional information from travellers, which wasn't required for the NZeTA request.
A traveller from Canada, Andrew Robertson, said he was charged double the visa cost and 400 per cent more in "handling fee", costing him $157 in total.
"While this scam is entirely legal, I am angry at NZ for allowing this to happen before I have even started my holiday," said Robertson, an engineer from Vancouver.
"It leaves many visitors with a bad taste in their mouth before even arriving in New Zealand, and I suspect many are alighting in Auckland with a similar feeling of discontent."
Shin Yamada, a visitor from Japan, said he turned to a third-party site after finding INZ's official site "too hard to use".
"I was travelling with my wife and three children, and we have to apply one by one and cannot do as a family," he said.
"Also, we have to key in many times because the system keeps rejecting our passport numbers. In the end we gave up."
Yamada said he ended up paying five times more than he should have, but felt he was left with no choice due to INZ's "substandard app and website".