The Transport Agency says it is dealing with almost 100 vehicles with flawed emissions data under the Clean Car Discount Scheme.
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The motor industry says it is finding rebates and fees being miscalculated.
On Wednesday, Waka Kotahi told RNZ it was aware of just two vehicles with problems, but now says it has 96 out of 4300 vehicle registrations.
"Fifty-six of these cases have been resolved by Waka Kotahi's dedicated team assigned to do this work," a spokesperson said.
"The majority of these are used vehicles imported from Japan which have multiple levels of sub models that require manual checks."
But problems are also cropping up before vehicles are registered, when importers and dealers try to ascertain if the NZTA data about emissions is correct. RNZ is aware the agency was already dealing with 95 vehicles like that at the start of the week.
The industry is also expecting more problems with European used cars.
"Overall the system is running well," Waka Kotahi said on Friday. "We've experienced some bedding in issues ... as expected with any new process.
"Waka Kotahi has been aware of the potential for some issues with historical CO2 data for some vehicles, which is why the [https://www.nzta.govt.nz/resources/rules/vehicle-efficiency-and-emissions-data-2022/?category=59&subcategory=34651&term=
Vehicle Efficiency and Emission Data Rule] was developed and shared with industry, setting out a hierarchy of testing cycles to calculate the CO2, along with a process for industry to request a review of the CO2 if they think it's incorrect."
Vehicle Importers Association senior advisor Kit Wilkerson said he was providing technical help to NZTA.
"The thing I am worried about is the potential that there's a lot of people that are being charged incorrectly out there, and the way the system is currently set up, NZTA is authorised to use the best data that they have at the time," Wilkerson said.
"So once the vehicle is registered, there's no going back.
"My biggest concern is the ones that we're not finding. I'm afraid people may just be saying, 'Oh, damn, this is what I'm stuck with', and paying it."
RNZ has asked NZTA to clarify the extent of any and all data problems impacting the scheme.