His resignation comes as Ports of Auckland and the Maritime Union square off in the Employment Court over their long running industrial dispute.
The union is arguing the port's early-March decision to contract out 292 union members' work to contracted stevedores was unlawful.
Justice Barry Travis has issued an injunction against the action until mid-May.
There was a "seriously arguable" case that deciding to contract out the workers' jobs undermined bargaining on a new collective agreement, while bargaining was still underway, his decision said.
Yesterday, 195 union members came to the port to accept its offer of a week's pay while issues around a return to work were before the court.
In a statement, the company said that was fewer than expected.
The port said the need remained for modern, flexible work practices to significantly increase productivity at its container terminals.