The worker trapped in his car when a shipping container was blown over and landed on it overnight has been discharged from hospital and is doing "all right".

Meanwhile, workers at the Ports of Auckland have spent today cleaning up the mess after last night's tornado wreaked havoc along the waterfront.

Ports of Auckland spokesman Matt Ball said the worker was trapped in his car on Jellicoe Wharf on Tinley St after a container fell on it. He had been discharged from hospital and did not require further treatment.

The man was an employer of stevedoring company Wallace Investments.

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Andy and Viv Stewart's 60ft catamaran Rosella was flipped upside down as wild weather tore through Westhaven Marina last night. Photo / File
Andy and Viv Stewart's 60ft catamaran Rosella was flipped upside down as wild weather tore through Westhaven Marina last night. Photo / File

About 30 containers, a mix of full and empty, were bowled over at both Jellicoe Wharf and the Fergusson Container Terminal.

Staff had spent today using a crane to lift the containers and the work was still ongoing this afternoon.

"Of note, last night one of the containers was actually flipped upside down. That's just an indication of the wind."

Ball said it was not unusual for empty containers to fall over in strong wind gusts.

Ports of Auckland general cargo operations is run by independent stevedores such as Wallace Investments who carry out the work for the shipping companies.

Wallace Investments has been contacted for comment.

Repairs to The Cloud are also underway after a roof panel at the mezzanine side was torn off and a side door broken when high winds hit the Auckland waterfront late on Sunday night.

Auckland Live director, Robbie Macrae, said clearing of debris from the area continued and while the total cost of the cleanup and repairs was still unconfirmed, it was expected to be at least several hundred thousand dollars.

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Shed 10, which was also damaged during the wild weather, is expected to be ready for reopening in time for the next cruise ship arrival on August 25. The Cloud will reopen ahead of its next scheduled event in mid-September.

Several yachts at Westhaven Marina broke their moorings and a catamaran was overturned in the turmoil.

One couple spoke to TVNZ about their devastation losing their 60ft catamaran Rosella which flipped upside down during last night's havoc.

Phil Goff inspects a shattered window pane. Photo / Tom Dillane
Phil Goff inspects a shattered window pane. Photo / Tom Dillane

Andy Stewart, who owns Rosella with his wife Viv, said when they got the call they couldn't believe it.

"I came down yesterday and checked all the lines and made sure there were double lines on due to the stormy weather around, but they reckon we had winds through here over 200km/h, so it just tore everything to bits and took off."