"There were 24 people inside the minibus, 16 people died including the driver, the rest are still being treated at hospitals," Jakarta police spokesman Muhammad Iqbal told AFP.
The transport ministry spokesman JA Barata said that a team from the ministry and the National Transportation Safety Committee would be deployed to investigate the cause of the crash, the spokesman added.
Eva Chairunisa, a spokeswoman for train operator Kereta Commuter Line, said the accident happened shortly before 9am when a train slammed into a packed minibus as it crossed a railway line in the north of the city.
"No one on the train was hurt in the accident but several bus passengers died," she said.
Chairunisa said the train driver followed standard procedures and sounded the horn to warn the bus before the accident happened.
The line was partially closed following the collision.
Transport accidents are common in Jakarta, where roads are heavily congested and buses and trains are often old and badly maintained.
In 2013 seven people were killed and scores more injured when a commuter train collided with a fuel tanker at a level crossing in Jakarta and burst into flames.
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