Tuesday’s crash saw a speeding train ram into a stationary one at a station near Arakkonam, about 55 miles (90 kilometres) from Chennai, in the southern state of Tamil Nadu.
Emergency teams worked Wednesday to clear the crash site, where five coaches were derailed in the impact.
“Initial reports suggest that the driver may have jumped the signal,” Railway Minister Dinesh Trivedi, who visited the scene, told reporters.
Southern Railway general manager Deepak Krishnan said the driver, who survived the crash, had ignored speed restrictions close to the station.
“He passed a few signals and then jumped out of the train and injured himself,” Krishnan said. “It is very difficult (to know what happened), we will find out the details.”
All the fatalities and injured passengers had been freed from the mangled wreckage by the morning, and engineers were working in heavy monsoon rains to repair the damaged track.
“I heard a loud noise but did not know what happened. There was no light and there was smoke all around. First we though it was a bomb blast,” Ramamurthy, 49, who only uses one name, told the Press Trust of India news agency.
“I heard the sound and in a flash I found myself lying on the track. Then co-passengers helped me,” he said after being taken to the local public hospital.
The line between the port city of Chennai and the town of Vellore was due to be re-opened by Wednesday evening.
India’s creaking state-run railway system — still the main form of long-distance travel despite fierce competition from private airlines — carries 18.5 million people every day.
While new shiny airport infrastructure is springing up across the country, the Indian railways — a much romanticised legacy of British colonial rule — often appear stuck in a time-warp.
After decades of under-investment, the rolling stock is old, speeds are low, signalling is done manually in some areas, and a lack of fencing makes the network a soft target for militants.
Experts say the system is desperately in need of new investment to improve safety and help end transport bottlenecks.
The last major accident occurred in July when a packed express train travelling from Kolkata to New Delhi derailed at high speed in the northern state of Uttar Pradesh, killing 63 people.
India’s worst rail accident was in 1981 when a train plunged into a river in the eastern state of Bihar, killing an estimated 800 people.