The collision between a commuter train and a long-distance train happened late on Monday in Bekasi, just outside Jakarta.
Bobby Rasyidin, chief executive of Indonesia's state railway firm PT KAI, said the death toll had risen to 14.
Mohammad Syafii, the head of Indonesia's search and rescue agency, said on Tuesday that the evacuation had been completed, adding it had been a delicate process to rescue trapped passengers from the mangled carriages.
"We needed to involve personnel with certain skills to perform a measured extrication," he said, adding there were no more passengers to find.
A women-only carriage bore the brunt of the crash.
Syafii said all the victims were women and most of them had been pinned by crushed metal.
Before disengaging the trains, rescuers were seen using angle grinders to cut through the metal of the compartments and reach the survivors.
Bobby told an earlier media conference that the commuter train first collided with a taxi on the tracks and was then hit by the long-distance train.
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.
Heriyati, a passenger, said she initially intended to use the women-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.
On Tuesday, 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
