The decision follows the death of a passenger after he was hit by a stone thrown at a train.
As the first steps, armed guards have been stationed for the night mail and intercity trains.
However, within two days of their deployment, seven instances of stone throwing have been reported.
In one incident at Moratuwa, several fishermen have been arrested on suspicion, while a group of youths is in custody over another at Kollupitiya.
Meanwhile, the movement for the protection of consumer rights has written to the transport minister, asking him to ensure the safety of train passengers.
The letter also calls for justice for the deceased passenger, who was a deputy director of education in the north central province.