Passengers are being given loo breaks at stations because of cloased toilets on an £850 million fleet of new trains.
Guards are making longer stops because toilets on some of South Central's latest carriages are locking people out.
Ageing slam-door trains on the London to Brighton and Sussex coast lines are being replaced.
The modern toilets lock automatically when they need emptying because new regulations stop waste being drained on to the track.
It can now only be disposed of at the end of a journey.
A South Central spokesman said passengers had on occasion been allowed to get off to use toilets at stations, although the company was trying to improve the train toilets.
New trains are already running between Seaford and Portsmouth, on the Brighton main line to London and between Brighton and Hastings.
South Central has already run into trouble with the trains because there was not enough power in the tracks to put them into service.
The company has had to put 100 of the £1 million carriages into storage.
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