Commuters and holidaymakers faced long delays after a rogue wave hit a train at Dawlish, Devon, this week.
The main railway line is still vulnerable to storms in spite of £35 million of repairs, according to the Western Morning News.
The Bristol to Plymouth Cross Country train was stalled on Monday and Network Rail says it cannot do anything to prevent similar incidents happening again.
Back in February, a four-mile stretch of the track at Dawlish was severely damaged by storms, with some of the line left hanging in the air after the sea wall was demolished.
The damage caused months of disruption to rail services west of Exeter and cost millions of pounds in repairs.
Cross Country spokesman Richard Gibson said its new Voyager trains were vulnerable to seawater because air intakes in the roof allow water to get into the electrics.
The company has an agreement with Network Rail and the Met Office that it does not operate at Dawlish when high waves are predicted, but there was no forecast of high waves on Monday.
A Network Rail spokeswoman told the Western Daily Press: "Our control room can confirm that the train was struck by a wave on Monday at Dawlish. This happens from time to time and is nothing unusual given the location of the railway line and its proximity to the sea wall.
"Normally it isn't a problem and trains can carry on as normal, as other than Cross Country, other train services are equipped to deal with salt water. However Cross Country trains aren't.
"We have a long-standing agreement with Cross Country that if bad weather is expected we will notify them and they will not run services on the line. We didn't have any notification of bad weather and therefore it appears that this was a rogue wave."
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