A total of 341 new trains ordered by the French train operator SNCF in a deal worth more than $4 billion (or 2.43 billion pounds) are too wide for many platforms, the media reported Wednesday.
Of the total 8,700 platforms, 1,300 will need to be modified to accommodate the new trains, Sky News reported.
"We discovered the problem a bit late, we recognise that and we accept responsibility on that score," a spokesperson for national operator RFF was quoted as saying in a radio programme.
Work has already begun to modify hundreds of stations that need cutting back to accommodate the new trains that will be rolled out from 2016.
SNCF said that 40 million pounds have already been spent to get the procurement back on track.
It added that the trains "were wider to meet public expectations" and that the alterations would cost just 1.25 percent of its annual maintenance and infrastructure budget.
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French Transport Minister Frederic Cuvillier said an "absurd rail system" caused the error.
"When you separate the rail operator from the train company... this is what happens."
The mistake was first reported by French magazine Le Canard Enchaîne.
The decade-long expansion plan comes as the rail system has seen a 50 percent rise in passenger numbers around the French capital, and a 40 percent rise in regional travel.