Officials said the train was going from Edirne Province to Istanbul when five cars derailed.
Transport Minister Ahmet Arslan said seven other trains had used the route earlier Sunday but the rain caused "extraordinary swelling".
The train, which was carrying more than 300 passengers, was heading to Istanbul. A statement from the prime minister's office said a suburban train suffered an accident after a landslide.
Over 100 ambulances have been sent to the scene, TRT Haber said, quoting Health Ministry Undersecretary Eyüp Gümüş.
The Ministry of Transport, Maritime Affairs and Communications said in a statement the accident happened after the railway track slipped down from its original spot due to heavy downpour.
A photograph of the site showed collapsed ground under the rails.
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According to reports, the train was travelling from Uzunkopru to Instanbul and came off the rails in the Tekirdag Corlu district.
President Recep Tayyip Erdogan has been informed over the accident and expressed his condolences over those who lost their lives, state-run Anadolu news agency said.
Turkey's audiovisual authority RTUK later said the government has issued a temporary ban on broadcasting images from the scene.
Turkish passengers have in general preferred taking planes or the bus for inter-city travel but this is changing with the new high-speed lines.
Turkey's rail network has been hit by several fatal accidents over the last years.
An overturned train auto is seen near a village at Tekirdag Province, Turkey, on Sunday, July 8, 2018.
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