Stan Semenoff said the Agency had "got it wrong" in the first place and the letter confirmed that.
"We need to operate within the law we have no problem with that and that's what they are there to do," Semenoff said in response to the decision.
In March 2019 the Agency announced it had revoked the transport service licence for SSL due to a continuing failure to address safety concerns.
However, SSL successfully appealed a decision to revoke the licence and 75 trucks remained on the road until the case was to be heard in court.
Two audits by NZTA revealed concerns relating to driver fatigue and behaviour, and included breaches of work-time and rest-time rules, pervasive logbook issues and the accumulation of 116 speed and traffic-related offences over a four-year period.
At the time SSL said the company did not consider NZTA had good grounds for its decision to revoke its licence and there had never been any serious safety concerns at the firm.
The latest decision not to revoke the transport licence comes as another NZTA investigation, challenged by SSL in the High Court, has seen the company issued with an assessment for unpaid road user charges for $532,878.96 over a 10-month period.
NZTA analysed records for around 17,200 loads carried by Semenoff's vehicles and found the truck and trailer units were travelling above their maximum allowable weight on about 68 per cent of the trips — 11,690 trips —based on the records that were provided between July 2016 to April 2017.
It was submitted on behalf of SSL the methodology used by the Authority was "totally arbitrary and bears no relation to the actual distance travelled overweight".
SSL appealed the decision of the District Court in the High Court which dismissed the appeal and said the District Court did not err in law.
In response Stan Semenoff said the case was "not over yet".
"I, like most hard working Kiwis, am very grateful for our courts and justice system. I respect the judge on her decision making regarding our case," Semenoff said.
"But my experience over my lifetime is that judges can sometimes get rulings wrong. The methodology used to reach this ruling was not appropriate and we stand by that."