None of the 220 passengers on board were injured in the incident, emergency services said.
"Everything is fine," said emergency services workers at 7.45pm on Wednesday evening, according to the Spanish edition of the Huffington Post.
Normal service has now been restored on the line, a spokesperson for Spain's national railway company Renfe told The Local.
The local mayor of Alpera, where the incident occured, said heavy downpours could have caused the problem.
National railyway infrastructure firm ADIF later said the train hadn't actually derailed but had been forced to stop because of a build up of water on the tracks.
The train was stopped because of safety fears.
Twenty Spanish provinces in central and northern Spain are on alert today with storms and heavy rain being forecast.
In July 2013, a high-speed train came off the tracks near the Spanish city of Santiago de Compostela in July 2013 killing 79 people people.