The Transport Agency chairman Michael Stiassny has announced his resignation.
His resignation comes six months, after revelations NZTA had not been properly checking up on companies which certify vehicle safety and give out licences.
The agency's chief executive Fergus Gammie also resigned in December.
Mr Stiassny said in a statement that he has completed what he set out to do, repositioning the agency to focus on public safety.
"The time is now right for a new chair and new permanent CEO with the skills required to guide the necessary culture change within the Agency to ensure public safety is at the heart of its function."
Transport Minister Phil Twyford has acknowledged his decision and thanked Mr Stiassny for his service.
He said Mr Stiassny worked tirelessly to not only uncover, but to resolve systemic failures within the Transport Agency.
"As a result of his leadership over the past year, New Zealanders can have confidence that the Transport Agency is fully focused on ensuring public safety on our roads," Mr Twyford said.
But National Party transport spokesperson Paul Goldsmith said Mr Stiassny's resignation just one year into his three-year contract points to internal chaos at the country's lead transport agency.
He said regional roading funding has been stripped bare and there has been a period of inaction and instability over the last 18 months.
"We've heard lots of concerns from mayors around the country that nobody is getting back to them, nothing's being done, things have been changing every few weeks."
Mr Goldsmith said Transport Minister Phil Twyford needs to get the agency under control.