The collision occurred at around 8:45 p.m. (12:45 GMT) when one of the trains, which was empty after being repaired, collided head-on with another train.
The other train was on the same track carrying 213 passengers as it traveled in the opposite direction, police chief Mohamad Zainal Abdullah said.
The accident left 47 seriously injured and 166 minor injuries.
No deaths have been reported to date.
Many were taken to hospital for treatment while the less seriously injured were treated at the station by paramedics.
The accident occurred in a section of tunnel about 100 meters (330 feet) from the KLCC station outside the Petronas Towers in the capital Kuala Lumpur.
“We are still investigating the incident…, but we suspect that there may have been miscommunication from the train operations control center,” Mohamad Zainal said.
Videos and photos of the incident posted on social media showed several bleeding commuters and broken glass panels inside the trains.
People can be heard crying in the background as they hug their bodies in pain.
Other more graphic videos show people lying on the floor crying in agony as blood runs down the aisle.
Some of the injured were taken out of the train and out of the tunnel on stretchers carried by paramedics.
Prime Minister Tan Sri Muhyiddin Yassin ordered the Ministry of Transport to conduct a full investigation into the crash, Malay Mail reported.
“I take this accident seriously and have ordered the Ministry of Transport and Prasarana Malaysia Berhad to conduct a full investigation to identify the cause of this accident, and severe measures must be taken immediately,” he said. in a press release.
“I understood that security and emergency personnel were on the scene. Hopefully the rescue operations go smoothly and the passengers involved are safe, while the injured receive immediate treatment.
“Priority must now be given to accident victims, and I have called on all parties to cooperate fully to ensure victims receive comprehensive treatment, as we are also in the midst of a growing wave of Covid pandemic. -19. “