The rescue operation had been completed with the death toll at 9, Divisional Railway Manager Anil Kumar Agarwal told reporters at the accident site, near the border of Karnataka and Tamil Nadu, about 45 kms from Bengaluru.
Five men, three women and a 9 year-old are among those killed in the mishap.
Railway Minister Suresh Prabhu said in a tweet soon after the accident that a boulder fell on the track and the train hit it.
Karnataka Director General of Police (DGP) Lalrokhuma Pachau said 16 passengers had been hospitalised, adding, "the rest of those with minor injuries were given first aid and they have left the place."
Railway police Additional Director General of Police R P Sharma said 25 passengers had received minor injuries.
The Bangalore-Ernakulam Inter City Express train had left Bengaluru at 0615 hrs and derailed at 0735 hrs between Anekal Road and Hosur on Bangalore City-Salem Section.
Prabhu said an inquiry had been ordered to fix responsibility and for corrective action to prevent such unfortunate accidents. He said he was monitoring "action" regularly.
Union Law Minister D V Sadananda Gowda, who was asked by Prabhu to rush to the accident site, said nine coaches had derailed. The injured had been taken to hospitals in Anekal and Bengaluru, he said.
Karnataka Health Minister U T Khader said here that medical teams were rushed from Karnataka and Tamil Nadu.
He said according to information available with state authorities, more than 50 people were injured.
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