Six bogies of the Gorakhpur-bound train were damaged in the accident which occurred at around 10 AM, railway officials and district administration said, adding the toll is likely to go up.
"We have confirmation of nine dead and over 82 have been injured. An inquiry has been ordered," Chairman Railway Board Arunendra Kumar said, adding, the exact cause of the accident is yet to be ascertained.
Local officials earlier said that at least 20 people were feared dead.
Modi spoke to Cabinet Secretary Ajit Seth and asked him to take an overview of the situation to ensure timely assistance to the injured.
Railways has declared compensation of Rs one lakh to the next of the kin of dead and Rs 50,000 for those who sustained grievous injuries, besides Rs 10,000 to passengers who suffered minor injuries.
CPRO of North-Eastern Railway Alok Singh said the train derailed and the bogies crashed into the goods train, which was standing on the adjoining track.
District Magistrate Bharat Lal said that six bogies were affected in the accident. He said that assistance of paramilitary personnel was being taken in the relief work.
Rail traffic between Delhi and Gorakhpur has been affected and a number of trains have been diverted through other routes, railway officials said.
Sant Kabir Nagar is about 242 km from Uttar Pradesh capital Lucknow and over 700 km from national capital Delhi.
Emergency helpline numbers in Delhi and Gorakhpur have been activated.
Kumar said the inquiry would be carried out by the Commissioner of Railway Safety North East Circle P K Bajpayee.
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