In a statement, Southern Rail said an alarm was activated on the 12pm Hastings to Brighton service between Hastings and Eastbourne, and it came to a stop while the matter was investigated.
As a precaution, the affected service moved backwards in order to let the following services through. This is has taken place now and services are now moving again, Southern said.
All lines have reopened following a fault on a train between Hastings and Eastbourne. Train services running to and from these stations may still be cancelled or delayed by up to 45 minutes.
Disruption is expected until 4pm.
Tickets will be accepted on Brighton and Hove Buses buses between Brighton and Eastbourne.
Railway users took to Twitter to complain that the delays would affect them seeing the World Cup match between England and Sweden this afternoon.