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Gammie has been under fire since it was revealed that the NZTA had not been carrying out its regulatory function properly, resulting in thousands of vehicles so far having to be retested for warrants of fitness.
In a statement, Gammie said that by stepping aside he was hopeful that the necessary review and improvement of the regulatory function at the NZTA could be completed without any distraction.
"As I said in October, the Transport Agency has long been focused and reliant on education and self-regulation rather than focusing attention and resources on ensuring regulatory compliance and enforcement. I also said that the public can expect that an increased number of enforcement actions would be taken to ensure compliance," Gammie said.
"In resigning, I note that the approach and focus of the Transport Agency has necessarily changed. I ask that full support be given to the board, management team, and Meredith Connell as they work towards resolving the outstanding issues and towards developing a stronger regulatory enforcement framework to ensure the public has confidence in the Transport Agency's processes," Gammie said.
In mid-October, the NZTA board, with the Minister of Transport Phil Twyford, announced an extensive review of NZTA compliance files by law firm Meredith Connell was under way and a tougher enforcement regime was being implemented.
Meredith Connell is currently leading the regulatory function at NZTA.
A spokeswoman for Twyford said today it was an operational issue for the NZTA board and inappropriate for the Minister to comment.
The issue of dodgy WoFs has been linked to at least one death, that of 65-year-old William Ball who was a front seat passenger in a car which lost control and crashed into a ditch on State Highway 12 near Turiwiri, Dargaville.
He died 26 days after the crash.
Police investigating the crash found the front seat passenger seatbelt was frayed and failed in the crash.
NZTA said Dargaville Diesel Specialists (DDS), who had issued a WoF to the car in December 2017, admitted it had done so without properly inspecting the vehicle, in particular the seatbelts.
The NZTA has engaged Kristy McDonald QC to conduct an inquiry into the case.
Since the announcement in October, the NZTA has been suspending a number of operators, with the number of dodgy WoFs issued up to 20,000 so far.
Nevertheless, Gammie said today he was proud of the work he had overseen during his tenure as CEO, "particularly setting NZTA on a path towards being a modern multi-modal transport agency.
"This has included establishing New Zealand's first light rail project, setting up a new safety & environment directorate to push forward safety outcomes, piloting new digital mobility solutions in Queenstown and Auckland, while reopening State Highway 1 from Picton to Christchurch in December 2017 one year after the mountain moving Kaikoura earthquake."
Gammie, who has had a career in the transport sector, including in NSW and Auckland, will step down on December 31.
The NZTA will make an announcement regarding the recruitment of a new chief executive in the new year.
Comment has been sought on Gammie's departure from NZTA board chairman Michael Stiassny.