The incident happened when the two wild elephants from nearby forest were crossing the track near the Madha tea garden between Hashimara and Hemiltongonj, deputy field director of Baksa (West) forest range Apurba Sen said.
The seriously injured animals succumbed to their injuries, he said.
The pachyderms were hit by a Guwahati-bound train from New Delhi carrying army personnel.
The Siliguri-Alipurduar section was blocked following the incident and long distance trains were diverted through another route, railway officials said.
The driver, assistant driver and gateman of the level crossing were being questioned, they said.
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