The elephants were killed when the Guwahati-Tinsukia Intercity Express hit the herd crossing the railway track at Venuguri village near Moriani Railway Station, officials said.
The elephants were returning to their nearby habitat Gibbon Wildlife Sanctuary.
While an adult elephant was cut into pieces, a calf died after it was hurled about 500 metres away due to the mishap.
Another adult elephant was found dead lying near the train track, they said, adding, forest personnel have rushed there.
Train movement was briefly disrupted on the route.
A tiger, which had strayed from a sanctuary, was also recently killed after being hit by a train while another elephant was killed at the same spot about six months ago.