The Lucknow-Barauni Express was changing tracks late Tuesday when it was hit from behind by the Krishak Express in Uttar Pradesh state, throwing carriages onto their sides, said spokesperson Anil Kumar Saxena.
"The death toll stands at 12. Another 45 people are injured," Saxena said.
The driver of the Krishak Express has been suspended for overshooting the signal, the spokesperson said.
Rescue workers, using metal cutters and other equipment, have retrieved trapped bodies while others were clearing the site and repairing the damaged tracks near the station in the city of Gorakhpur.
Railways Minister Sadanand Gowda said human error appeared to be the cause of the accident, with an official inquiry underway.
"It's (the) loco pilot's mistake, who neglected the signal. The loco pilot has been suspended, strict action will be taken for negligence," the minister wrote on Twitter.
TV footage showed sandals, clothes, bottles and suitcases strewn through one of the destroyed carriages, whose roof had almost completely caved in.
"We were sleeping when we heard a loud bang followed by a massive jolt," Ram Kumar Chaudhary, a passenger on the Lucknow-Barauni Express who was injured in the accident, told TV networks.
"The next thing we saw was that the passengers were piled one on top of the other and the coach was lying on its side."
Trains are running packed in northern India in the lead-up to the major Hindu festival of Dussehra on Friday, a national holiday.
Deadly accidents are common on India's railways, whose vast and rundown network carries tens of millions of people daily.
In July 20 people were killed, most of them children, when a passenger train rammed into a school bus in southern India.
A government report in 2012 said almost 15,000 people were killed every year on the network. It described the deaths as an annual "massacre" due mainly to poor safety standards.
In another accident reported from Utta Pradesh an army helicopter crashed near Bareilly Wednesday and killed two pilots and an engineer, the Press Trust of India news agency said.
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Someone should come up with driverless trains ....... trains that will run automatically without drivers and would also have the capability to scan the tracks, look for obstacles ..... miles and miles ahead to see if everything ahead is safe and sound and, where ever necessary, take corrective actions. Google has come up with a car and such trains will not be far away. Some day later, even pilotless passenger planes will ferry passengers and freight just like the unmanned drones.