Four baby elephants and two adults died in the collision near Minneriya, about 200km from the capital, Colombo.
The area is renowned for its nature park and wildlife, said Hasini Sarathchandra, a spokesman for the government's wildlife department.
Local television channels showed the train engine and several compartments had derailed following the collision.
No passengers were injured, said a railway official, who declined to be named because he was not authorised to speak to the media.
Sarathchandra said the wildlife department was investigating the incident.
Minneriya National Park draws thousands of tourists each year hoping to see elephants in their wild habitats.
It is part of the "elephant corridor" that connects Kaudulla and Wasgamuwa National parks.
Train collisions involving elephants have increased in recent years in Sri Lanka, with wild elephants attempting to cross railway tracks in search of food and water.
They are increasingly vulnerable because of the loss and degradation of their natural habitat and many venture closer to human settlements in search of food.
Some are killed by poachers or farmers angry over damage to their crops.
According to government statistics, nine elephants died in 2024 after being knocked down by trains, compared with 24 in 2023.
Though elephants are revered in the Indian Ocean island nation, they are endangered with their numbers dwindling from about 14,000 in the 19th century to 6000 in 2011, according to the country's first elephant census.
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