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.
The container that blew on to the railway line is believed to have come from a yard operated by CSL Containers on the eastern side of the railway line just north of the Otahuhu train station.
"It [the train] was kept in the station overnight, so it must have been very close to the station," Hannan said.
"There was a little bit of damage to the train and the overhead power wire looks like it was knocked down by the container as it came down."
He said the damaged train was removed mid-morning on Sunday. Train services continued using one of the two southern rail lines, and normal services were resumed on the other line at 1.05pm on Sunday.
Hannan said the container was empty. A standard empty 20-foot (6.1-metre) container weighs 2.3 tonnes (2300kg).
He said Auckland Transport had notified the incident to KiwiRail, which owns the tracks and overhead wires.
WorkSafe and the Transport Accident Investigation Commission both said they had not yet been notified, but that they would not expect to be told until tomorrow because there was only minor damage.
Dearsly said the two incidents at Otahuhu and Wiri followed other stacks of containers toppling in Christchurch and Wellington in the recent earthquakes.
"There are standards for stacking and storage but I don't think it extends to stacking a string of containers," he said.
"The way health and safety should be done is not to say you can't do something, it's to identify the risk and put in place appropriate controls. Each situation is going to be different."
CSL Containers general manager Jarrod Smyth said in response to written questions: "We are currently conducting an investigation into Saturday night so I have no comment to make on the below at this stage."