The derailment was caused by 'interference by outsiders,' Crimean railways said in a statement.
Fear and suspicion stalk the streets of Kherson, a southern port that was occupied by Russian troops for over eight months before they were driven out by Ukrainian forces.
An investigation was opened to confirm the cause of the crash, which occurred in the Dzhankoi region of northern Crimea.
An explosion was also heard following a missile attack that hit the Black Sea city of Odesa overnight, a local Ukrainian official said.
There were no immediate details of any damage from the strikes elsewhere on the Crimean Peninsula, which Russia annexed from Ukraine in 2014.
A spokesperson for Ukraine's southern command said the fire has caused a great deal of "anxiety" in the Russian military.
Kyiv almost never publicly claims responsibility for attacks inside Russia or on Russian-controlled territory in Ukraine.
Military analysts say Ukraine is likely soon to launch a counteroffensive and retaking all the Kherson region would be an important step.
A French official said on Monday that Shaye will receive a "very firm" update at the French Foreign Ministry on Monday.
Russia's TASS news agency quoted an adviser to Aksyonov, Oleg Kryuchkov, as saying that debris had fallen in a Crimean town.
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