Trains through Dawlish remain vulnerable to storms, despite the £35 million repairs to the track.
A Cross Country train was halted last week after it was hit by a wave at Dawlish, bringing delays of more than 35 minutes to morning commuters.
And now Network Rail admits that it cannot do anything to prevent similar incidents.
A four-mile stretch of track at Dawlish was severely damaged by storms in February this year. Part of the line was left hanging in the air after the sea wall was demolished. The damage caused months of disruption to rail services west of Exeter.
Last week the 6.34am train on Monday,from Bristol towards Plymouth, was swamped by a wave at Dawlish. Cross Country said its relatively new Voyager trains were vulnerable to seawater because air intakes in the roof allow water to get into the electrics.
A Network Rail spokeswoman said: '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.'
She said Network Rail was doing 'resilience' work in the Dawlish area, but added: 'This isn't really a resilience issue.
'Our work is to prevent what happened at the beginning of the year happening again, however we cannot help the fact that waves will hit trains - this will always happen due to the proximity of the line to the sea wall.'
Devon County Councillor Andrew Leadbetter, chairman of the Peninsula Rail Task Force, said: 'This is not entirely unexpected, and we are likely to see similar incidents in the future.
'It goes to show that as an absolute minimum the Dawlish line must be reinforced to withstand winter weather.
'The Peninsula Rail Task Force partnership is holding the Government to its pledge to ensure the line is resilient, as well as looking at additional routes.
'Any additional route will take time to implement, so regardless of future plans, ensuring safe and regular access in and out of the South West is vital, and that means ensuring Dawlish is able to withstand severe weather.'
Last month Network Rail's engineers started improvement work on the final section of seafront walkway between Rockstone and Coast Guard footbridges at Dawlish.
The work includes building a new protective wall and raising the walkway so that it can be used in all tidal conditions.
The walkway is closed until work ends in the new year.
