Crane three is getting a structural upgrade over the next two weeks, Port Otago general manager of marine and infrastructure Sean Bolt said.
"Crane three is undergoing some structural upgrades, so it’s going to be out of action for a couple of weeks while we do that."
Ships would be in about 1.8 times longer than normal, he said.
"All ships will have to because we’re only operating with one crane."
The crane work was planned after electrical and structural upgrades were carried out on the other crane last year.
Mr Bolt said this time of the year was usually quiet for the terminal so it was a good opportunity to do the upgrades.
Port Otago is unable to carry out electrical upgrades needed on crane three because it cannot get engineers from overseas to do the job as the border is closed because of Covid.
"The electrical upgrade will just happen at a later stage," Mr Bolt said.
