A metro train carrying 213 passengers collided with an empty one in a tunnel near the Petronas Towers, at about 20:45 (12:45 GMT), police said.
The empty train had just been repaired, and was going in the opposite direction on the same track as the full one.
District police chief Mohamad Zainal Abdullah told reporters there was no sign of foul play.
"We are still investigating the incident... but we suspect that perhaps there was a miscommunication from the trains' operation control centre," he said.
