The collision between a commuter train and a long-distance train happened late on Monday in Bekasi, just outside Jakarta.
Bobby Rasyidi, chief executive of Indonesia's state railway firm PT KAI, said the death toll had risen to 14 and that evacuation work was still ongoing.
Mohammad Syafii, the head of Indonesia's search and rescue agency, told a press conference on Tuesday that it was a delicate process to rescue survivors from the mangled carriages.
"We needed to involve personnel with certain skills to perform a measured extrication," he said. "There are some victims who are alive to this minute and we're hoping to extricate them, but they're still pinned by the train material."
Rescuers have disengaged the trains, a Reuters witness said. They were seen using angle grinders to cut through the metal of the train compartments and reach the survivors.
Bobby told the press conference the commuter train first collided with a taxi on the tracks and was then hit by the long-distance train. A women-only carriage bore the brunt of the crash.
Taxi operator Green SM Indonesia said on Instagram that the taxi involved in the accident was part of its fleet. It said it had sent information to authorities to assist in the investigation.
Green SM Indonesia is the Indonesian branch of Vietnamese electric-vehicle taxi operator Green and Smart Mobility JSC, an affiliate of Vingroup.
After visiting a hospital in Bekasi, President Prabowo Subianto said he had agreed to build a flyover near the train tracks to help resolve heavy traffic congestion, adding that authorities would investigate the collision.
He said large parts of the train network are not well-maintained.
Indonesia's National Transportation Safety Committee (KNKT) is investigating the crash.
On Tuesday, rescuers and people descended upon the train station, some looking for their relatives.
A man was seen crying while holding his brother's bloody bag. Heriyati, a passenger, said she initially intended to use the women's only carriage but opted for the one behind it.
She had been on a call with her husband asking him to pick her up from the station when the collision occurred.
"I haven't even finished with the call and the trains collided," she said.
Commuter line trains are some of the busiest in Jakarta, the world's most populous city. On Tuesday, PT KAI said several commuter train trips were cut short due to the crash.
Land transport accidents are common in Indonesia. A train collision in West Java province in 2024 killed four people and injured dozens.
with AP
