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Three of eight directors have now resigned.
Transport Minister Phil Twyford said the agency was going through a massive change process and it was understandable there might be some movements on the board.
Board members Chris Ellis and Adrienne Young-Cooper have left, and the deputy chair Dame Fran Wilde will leave at the end of this month.
Nearly 25,000 people were contacted to get their vehicles rechecked after more than a dozen inspectors or garages were suspended for issuing dodgy warrants last year.
The transport agency's Fergus Gammie resigned in December, saying the move would allow a review of the organisation to be done "without any distraction".
Law firm Meredith Connell was appointed to oversee a review of 850 outstanding compliance files including a case where a Dargaville mechanic warranted a car which crashed a short time later killing a passenger whose seat belt failed.