Earlier this month the KiwiRail board reportedly appointed an external investigator to speak with departed managers following negative reports about Miller.
Late last month McCormack told the Herald in response to questions on the matter that the board supported Miller and his senior leadership team.
"The information you have been provided is incorrect and untrue. No instruction or appointment has been made or considered to review the management style and culture of KiwiRail's CEO," McCormack said on October 28.
In mid November, BusinessDesk reported the current board had in fact ordered a review to find out why people had decided to leave and to help ensure KiwiRail was a good place to work.
Miller said today in a statement he was proud to have led KiwiRail through a transformational period, including improved safety leadership.
"I wish Team KiwiRail well as they deliver projects which will see rail enjoy a greater role in New Zealand's transport sector in future."
Deputy chief executive Todd Moyle had been appointed acting chief executive and the board would begin a search for a permanent replacement, McCormack said.
- Additional reporting by Herald staff