The collision between a commuter train and a long-distance train happened late on Monday in Bekasi, just outside Jakarta, with a carriage reserved for women bearing the brunt of the crash.
Agus Harimurti Yudhoyono, Indonesia's senior minister for infrastructure, told reporters the death toll had risen to 15.
Mohammad Syafii, the head of Indonesia's search and rescue agency, said all the victims were women and most of them had been pinned inside by crushed metal.
It had been a delicate process to extricate them from the mangled carriages, he said, but the evacuation had been completed.
Before disengaging the trains, rescuers were seen using angle grinders to cut through the metal of the compartments and reach the survivors.
Transport Minister Dudy Purwagandhi said the crash took place after a taxi stopped on a crossing near the Bekasi Timur station, state news agency Antara reported.
The commuter train was held on the platform where it was then hit by the long-distance train, the report said.
Taxi operator Green SM Indonesia said on Instagram that the taxi 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 one of the Bekasi hospitals treating the injured, President Prabowo Subianto said he had agreed to build a flyover near the railway tracks and that authorities would investigate the collision.
He said large parts of the train network were not well-maintained.
Indonesia's National Transportation Safety Committee (KNKT) is investigating the crash.
On Tuesday, people rushed to the station with some looking for relatives.
Heriyati, a passenger, said she had initially intended to use the women's only carriage but opted for the one behind it instead.
She had been on a call with her husband asking him to pick her up from the station when the crash happened.
"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, state railway company PT KAI said several commuter train trips were cut short due to the crash.
Adriansyah Yasin Sulaeman, an executive director of the think tank Forum Transport for Jakarta, said the government needed to improve the ageing railway network, including separating tracks for express long-distance trains and commuter trains.
"These commuter trains are a symbol for the working class," he said.
"It's a big alarm for the government to seriously improve it."
Land transport accidents are common in Indonesia.
A train collision in West Java province in 2024 killed four people and injured dozens.
with AP
