The accident took place in the Lumding-Bardarpur Hill section under Lumding division.
The Northeast Frontier Railway (NFR) will run a special train to Bangalore on September 1 to ferry people back, who had fled from many parts of south India in panic over rumoured threats.
The 17-year old girl travelling with her uncle in a three-tier AC compartment raised an alarm at 4 am when the armyman was making an attempt to molest her as the Rajdhani Express was passing between Lumding and Chaparmukh stations, a NF Railway spokesman said.
The revised death toll is nine and 41 were injured.
Heavy rains in the last three days triggered flash floods in parts of Bihar, where 41 people have died so far, and inundated large areas in Assam and North Bengal, paralysing normal life and snapping rail link to the Northeast from the rest of the country.
After several delays, it will be completed by Jan 2017.
North East Frontier Railway officials said two unidentified male bodies were found from the coaches while six persons were injured in the derailment that occurred at around 9pm near Shamuktala Road station, about 32 km from Alipurduar Railway Division headquarters.
Life was hit in lower Assam for the second day on Tuesday in three bandhs called to press for Bodoland and Kamtapur, while Karbi Anglong, which had erupted over statehood demand on the lines of Telangana, was slowly limping back to normal.
Currently, the Brahmaputra at Guwahati, Nimatighat in Jorhat, Tezpur in Sonitpur, Goalpara and Dhubri towns, while the Barak at AP Ghat in Cachar and Badarpurghat in Karimganj are flowing above the danger mark.
Violent agitations continued to rock parts of West Bengal for second consecutive day on Saturday as people protesting against the amended Citizenship Act set several buses on fire and torched portions of a railway station complex, officials said.
With the recovery of four more bodies today, the death toll mounted to 36 in Assam floods that affected about 10 lakh people in 13 districts and rendered majority of them homeless.
A day after total shutdown in Assam to protest against the CAB, fresh protests erupted in the state and neighbouring Tripura and other parts of the nation.
'The prime minister expressed concern and assured all possible help to the state,' CMO said.
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