The train's two engines and 25 empty cement cars were thrown from the tracks along a heavily travelled north-south rail corridor in the northern state of Perak, according to a statement by rail operator KTM Berhad.
Remarkably, the only casualties in the accident were the train's conductor and his assistant, who were slightly injured, local media quoted police as saying.
KTM Berhad said two rail lines were blocked by the resulting pile-up of train cars.
However, a KTM spokesman quoted by the New Straits Times said about 12,000 commuters were affected and that some services would be halted for 48 hours.
KTM's statement said buses were sent to transport affected travellers.
No cause has yet been given for the incident.
Malaysia has an extensive rail network dating from the British colonial era and it remains an important and popular mode of transport for both passengers and cargo.
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