The train had departed Colbert Station in Limerick en route to Ballybrophy at 6.43am and was met by closed gates at a level crossing at Sallymount, Lisnagry, where the train ploughed through the gates.
Nobody was injured in the incident and at the time of the crash only the driver and guard were on board the train.
The two-piece commuter rail car costing €750,000 was delayed for more than 30 minutes at the scene as the driver contacted Irish Rail authorities.
There was only minor damage caused to the train.
Buses were provided to pick up passengers waiting at stations at Birdhill, Nenagh and Cloughjordan.
The train later went on to Ballybrophy and picked up passengers from Dublin travelling to Limerick.
A spokesman for Irish Rail said: “This is being regarded as a serious incident and a full investigation is now under way. There are a number of variables which will have to be looked into to ascertain what caused this.”
The investigation is being headed by Irish Rail’s district manager in Limerick, Jim Meade.
When the investigation is completed, he will send a report to the Irish Rail safety officer in Dublin.
Prior to the incident, the train had travelled through the automatic level crossing barrier on the main Limerick to Dublin N7 road at Lisnagry.
The gate at Sallymount, which is on a minor back road, is manually controlled.