Warrnambool line trains have been replaced by buses after the Sunday morning service hit an abandoned bike on the tracks.
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The 7.25am train hit the bike near the Sherwood Park Station at Deakin.
V/Line spokeswoman Catalina Filip said engineers were working to repair damage caused to carriages in the incident.
The 5.30pm service from Warrnambool to Southern Cross will be replaced by buses, but V/Line hopes the 7pm service from Melbourne will run as normal.
Ms Filip said the incident was an important reminder of the danger of leaving items on train lines.
“We encourage anyone who sees an object left on the tracks to report it to Victoria Police,” she said.