Ms Kaye said the problems had been "unfortunate". "ACC and NZTA are going to need to go back and learn from this."
But she said the benefits of the system would save lives, reduce serious injury and lessen the cost of accidents on taxpayers. She said the average cost of a serious injury accident was about $2 million while the anticipated lifetime cost of accidents last year was about $450m.
"If we can prevent just a couple of injuries, at a fiscal level it makes it worth it."
She said the New Zealand car fleet was not as good as that in other countries and effort needed to be made to improve it.
"If we can get more safe vehicles on the road there's real evidence of a reduction in serious injuries and fatalities."
It has also emerged a flat-rate for all motorists was passed over in favour of the more complicated new system. Officials told Ms Kaye all motorists could be charged $104.09 for all petrol vehicles.
She said the new system was intended to be fair, aligning cost with risk and charging more where there was a higher level of danger.
Ms Kaye said she expected the greater awareness of risk associated with certain makes of car would improve road safety. She said the discussion around the errors would also have benefits in making people more aware of the risks associated with their vehicles.
While the errors were clogging headlines, Ms Kaye said most motorists were drawn to the big reduction in cost. "It's unfortunate about the errors but everyone is being reminded of the overwhelming cuts."
Ms Kaye is the only minister to step forward even though associate transport minister Craig Foss has the responsibility for the overall system. His office would not be drawn, saying it remained an "operational" issue.
A NZ Transport Agency spokesperson confirmed "performance issues" with NZTA's connection to outlets -- such as Post Shops -- which handle car registrations. The problems meant "some transactions timed out or failed to respond".
The spokesman said the system needed to be started again on two occasions, taking the system offline for up to 15 minutes. The system was working normally from 2pm.
"We are still investigating what caused or contributed to the performance issues given our system is designed to support large numbers of transactions."
Motorists are able to renew their rego online at www.nzta.govt.nz/renew.