A V/Line spokesperson said the incident involving a grain train carriage derailing happened on the freight siding but that the train was blocking the main line used for passenger services.
The train has since been move back to the siding and the main line is clear.
The incident effected the 6:55am train from Swan Hill to Southern Cross and the 7:40am train from Southern Cross to Swan Hill. The 5:35am and 6:19am trains from Eaglehawk to Southern Cross were also altered and originated at Bendigo with alternate transport arranged for Eaglehawk passengers.
No other service changes are expected as a result of the grain train incident.
"We thank Swan Hill line and Eaglehawk passengers for their patience while we worked to get them where they needed to go following disruptions to their services this morning," the V/Line spokesperson said.
"Safety is our number one priority. We take all incidents seriously and will complete a full investigation into the incident at Mitiamo."
The V/Line spokesperson said the freight train will move out of the siding when it is safe. Once it has moved it will allow crews to repair track damage in the siding and allow normal freight train operations to resume.
The Office of the National Rail Safety Regulator has been advised of the incident.
Train tracks on the Swan Hill line have become damaged after they gave way underneath a grain train on Thursday morning.
Maryborough police attended the scene at Mitamo at 1.30am to find a grain carriage had become dislodged.
Sergeant Gary Walter said a train was shunting and hooking carriages together when the incident occurred.
"The tracks have given way and it's come to a stop," he said. "There were no injuries or major damage.Police were there for a couple hours to make sure everyone was safe and there were no other major issues.
"It happened when one train was hooking up other carriages. As it maneuvered, the tracks under it have given way. It was at very low speed.
"We believe the sleepers underneath have given way and rails spread causing one of the carriages to dislodge."
Swan Hill trains will be replaced with coaches for their journeys to Southern Cross following overnight damage to train track.
The Department of Transport said an overnight incident resulted in track damage and that repairs were likely to take some time.
Passengers travelling in either direction are urged to allow extra time for their journey.
"The Department of Transport thanks passengers for their patience as crews work to resolve the issue and restore normal service," the department said in a statement.
More to come
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