Car dealers are worried they will have to pay the bill for errors in the Clean Car Discount Scheme that could cost buyers hundreds or even thousands of dollars.
They say the fees or rebates the system calculates based on a vehicle's emissions are sometimes incorrect.
They also warn that the problems are more widespread than Waka Kotahi is admitting.
When Wanaka car dealer Rod Hicks sold a 2020 Toyota CHR hybrid, he was expecting the registry guy to call him on Friday, the first day of the Clean Car scheme, to confirm that the buyer would get a $1400 rebate.
"And he rings me up and says, 'I'm going to need $1854 extra from you'.
"I said 'why?'. He says 'it's got a fee on it'. I said 'no it hasn't, it's got a rebate'. So he goes 'no, the system here is telling me that's it, it's got a fee'."
Hicks asked Waka Kotahi for help; five days on, on Thursday it emailed saying there was a "known issue" and it was "investigating".
Hicks said he had 20 near-new cars in Japan awaiting import, and may face problems with 15 of them because his checks shows the Clean Car system lacks emissions data for them, defaulting to a high fee.
NZTA said on Wednesday the system "is running well".
It said it knew of only two cars nationwide charged a fee, when they should have got a rebate.
That surprised Lower Hutt Te Awa Kairangi car dealer Steve Bottrill, who was in touch with Waka Kotahi on Wednesday.
"That's interesting ... we submitted five vehicles to them that they had to change and update," Bottrill said.
On his yard he also has two identical Toyota Aquas, one with a $1600 rebate, the other showing a $1200 fee.
He has a BMW facing a $2400 fee, though his own checks show the car should pay half that amount.
And he has a half dozen Volkswagen hybrids that have hopped in recent days from a $2300 rebate, to a $2875 fee, to a $2000 rebate.
"The most frustrating part is we can't trust the data that's there," he said.
"And unless you are onto it, and know that something could be wrong, you won't know. So we are potentially misleading the public based on the information [from] NZTA.
"What happens when ... a customer gets charged a fee ... it turns out to be incorrect, who's liable for that?"
It is already costing Bottrill money; where he is not sure of the NZTA data, his dealership is paying $400 to $500 per car for a fresh Statement of Compliance.
Hicks said if NZTA refused to respond in his case, he would pay the $1800 fee himself.
"I have to. I've sold her a car at a registered, delivered price."
Dealers have till mid-April to display the correct fee-rebate information on each car they sell. Trade Me Motors is giving itself till the end of May.
Hicks said a compounding problem was the official information varies on the Rightcar and EECA websites for some cars.
Motorcentral, which supplies data services to dealers, told customers a few days ago it aimed to determine Clean Car fees but government services "have only recently been delivered to us which means we have had very little time to implement and test it ... it's obvious we will not be ready by the April 1st deadline".
It told RNZ it was working to get the services in place.
Transport Minister Michael Wood said in a statement that teething problems were expected with any new large scale programme.
"I am seeking assurances from Waka Kotahi that these are isolated cases and that there is a plan to remedy the problem," Wood said.
He and NZTA referred to 12,000 rebates issued so far as evidence the system was working well.
However, this counts from mid-2021 under the entirely different, rebate-only system, when no calculations around emissions were required.
Waka Kotahi yesterday once again said these were "bedding-in issues".
The Vehicle Importers Association was providing technical help, however, NZTA had not taken up its offer of access to the association's extensive database, its chief executive David Vinsen said.
"Remember we're in day six of this, and we were expecting a few initial niggles or implementation problems ... but nothing like this," Vinsen said.
"It's frustrating because we're in a situation of saying, 'we told you so'."
He is referring to years of lobbying government to fix the motor vehicle registry that is now feeding data to the Clean Car scheme.
"It's been cobbled together over many years. And that's the only information they had to rely on."
The problems would have been "a whole lot worse" if they had not worked with a dedicated NZTA team, "flat out" for months to backfill a "huge amount of gaps" - but they had not been able to plug them all, Vinsen said.
"I'm not blaming them, they're given a hand to play with.
"It's the minister's fault. It's not the officials' fault."
NZTA said some problems might be due to dealers entering incorrect or incomplete data or in other instances "the source data may be incorrect".
National transport spokesperson Simeon Brown said it might take urgent legislation to fix this.
Consumers "may be paying taxes which they shouldn't have to pay, and now there's no way for them to be able to get that money back again".
"The legislation makes it clear that once a car is registered there's no ability for that to be refunded if a mistake was made."
Wood said the expansion of the Clean Car programme was well signalled, and it would help "reduce the pain" at the pump.
Hicks felt like he was left doing clean-up.
"It is NZTA's fault ... it should've been tested properly. And it shouldn't have been introduced until it was all done."