The incident took place at Bamgaon Tea Estate in the Chariduar police station area near Balipara at 1.30 am, they said.
The herd was trying to cross railway tracks between the Rangapara and Dhalaibil stations when the Guwahati-Naharlagun Intercity Express hit them, Chief Conservator of Forest (Northern Range) P Shiv Kumar told PTI.
Four female elephants, including a pregnant one, and a male jumbo were killed on the spot, he said.
He said forest officials were trying to locate the other two elephants, which were part of the herd.
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The dead elephants were cremated after post-mortem examination, Kumar said.
Wild elephants often come out of the nearby Nameri National Park in search of food, he said.
In the last couple of days, a herd of around 70 elephants strayed into the area, near the accident site, a forest official said.