A shipping container weighing about 2.3 tonnes was blown on to the main trunk railway from a container stack at Otahuhu in the weekend storm - and was hit by a train just after midnight.
Auckland Transport spokesman Mark Hannan said the commuter train was returning to its depot when it hit the container at 12.08am on Sunday. No passengers were on board and no one was injured.
But Greg Dearsly of the NZ Institute of Safety Management said the incident dramatised the risks of stacking containers in high piles without securing them against high winds.
A WorkSafe spokesman said 12 containers also blew over in the storm at the Wiri container terminal, also without any injuries.
The MetService said the storm caused northeasterly wind gusts at Auckland Airport of up to 95km/hour - a "rare occurrence" for a northeasterly which is not the predominant wind direction in Auckland.