The decision follows a period of consultation with employees and customers.
From July the port will berth the majority of visiting container ships at its newly expanded Fergusson terminal, and base all stevedoring staff there.
Managing director Jens Madsen said the changes would streamline port operations.
"This is about steering the company through the current economic downturn, using our berths, land, equipment and labour as efficiently as possible, reducing cost and further lifting productivity," Madsen said.
"The changes will remove unnecessary duplication of overheads and infrastructure and further improve our ability to resource customer demand at peak periods. Under this new operating model we will be a leaner company, better positioned to capture sustainable growth once the recession is over."