The herd was walking across a newly upgraded railway line that runs through a jungle area when the accident occurred at Cheddikulam, about 260 kilometres north of Colombo.
"One of the baby elephants was dragged about 300 metres along the track after being hit," a local police official told AFP, adding that it was thought to be Sri Lanka's worst accident involving the animals.
No passengers were injured in the collision.
Although elephants are considered sacred in Sri Lanka and are legally protected, nearly 200 are killed every year, many by farmers after the animals stray onto their land.
In 2011, three baby elephants were killed by a passenger train along the same track in a forest area about 150 kilometres north of Colombo.
In May this year, four elephants including two calves were killed by lightning in the country's north.
Sri Lanka's elephant population has dwindled to just over 7,000, according to the latest census, down from an estimated 12,000 in 1900.
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