Three bright orange empty shipping containers that were blown into Wellington Harbour this afternoon have been safely retrieved from the water.

CentrePort tug boats and Maritime Police battled rough seas and strong winds for several hours to safely retrieve the empty containers.

Centreport said winds in excess of 100km/h in the capital had hampered efforts to recover the containers.

The three containers were blown into the water this afternoon off the south end of the container terminal at Wellington's CentrePort.

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Two of the containers were about 12m long and one was about 6m long.

Harbourmaster Mike Pryce said it was rare for containers to be blown into the harbour.

"I can't remember the last time, I think last time two blew off a container ship, but I can't recall them blowing into the harbour off the wharf before."