The incident happened when the elephants were crossing tracks in Potiyapam area of Kampur. The two tuskers died on the spot, district administration officials said.
Another elephant was battling for its life.
Train services were affected following the incident with the Dibrugarh-Delhi Rajdhani Express, Dibrugarh-Bangalore Express, Dibrugarh-Howrah Kamrup Express and Delhi-Dibrugarh Brahmaputra Mail held up at several stations, a North East Frontier Railway spokesman said.
The spokesman said the accident area was not earmarked as an elephant corridor.
Ten elephants have been killed by trains in the state during the month with seven dying in Nagaon district alone. Two were killed in neighbouring Karbi Anglong and one in Bongaigaon district.