"We have recovered 100 bodies so far. And some bodies may have been washed away" by the fast-moving floodwaters of the river, said Thomas Verghese, general manager of India's southern railway.
About 100 injured passengers had been rescued from the coaches, which derailed after floods washed away the tracks in the town of Veligonda in Andhra Pradesh state.
The injured had been flown by helicopters to hospitals in Hyderabad, the capital of Andhra Pradesh, local police Inspector General Govind Singh said.
Army divers and local volunteers swam to the coaches to help pull out the injured. Other soldiers, lowered onto the roof of the coaches by helicopter, used gas cutters to open the top of coaches and pull out people, who were hanging on to luggage racks and ceiling fans.
At least five of the trains cars
were on their side
Scores of passengers were trapped inside the coaches, at least five of which were lying on their side, partly submerged in water. One of the coaches was on top of another.
Railway officials were waiting for cranes to reach the accident site to lift the submerged coaches.
Track washed away
"We were fast asleep, when there was a big bang and a thud. The next thing the train was under water," said P Ramesh, a passenger, who lost seven members of his family, including his wife and brother.
"It was pitch dark and people were screaming," Ramesh said as he waited for soldiers to cut open the side of the coach and pull out the dead.
Heavy rains have lashed the
region for days
"I was able to clamber out of the coach, but others were not so lucky. They are still inside," he said.
The train - an engine and 17 coaches - hit a portion of track washed away by flash floods, and seven coaches derailed, officials said.
The heavy rains also washed away many roads in the area, making it difficult for rescuers and ambulances to reach the accident site. Traffic jams stretched for kilometres on roads leading to Veligonda.
Three days of heavy downpours caused at least three water reservoirs to breach their banks, triggering the flash floods, said R Velu, a federal junior minister for railways who visited the accident site.
Veligonda is 80km east of Hyderabad.
Railway workers attached an engine to the rear of the train and pulled the 10 remaining cars to a safer section of the track, said Esther Kar, a railway ministry spokeswoman in New Delhi.
"We were fast asleep, when there was a big bang and a thud. The next thing the train was under water"
Train crash survivor
Rains have battered southern India for more than a week, claiming at least 90 lives in Andhra Pradesh and the neighbouring states of Tamil Nadu and Karnataka. Most died due to drowning, electrocution and injuries caused by housing collapses.
India's sprawling rail network - 107,200km long - is the world's third-largest after Russia and China.
Every day, at least 13 million people use the state-run network, which has poor safety standards and is plagued by accidents. Around 300 accidents involving trains occur in India each year.