Some Bendigo V/Line services have been delayed up to 30 minutes on Wednesday morning.
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Bendigo V/Line tweeted a track fault between Sunbury and Watergardens stations caused delays before 7am.
The fault has since been cleared and services have resumed to normal.
Bendigo V/Line has urged commuters to still allow for additional travel time.
It comes as the latest performance data showed Bendigo trains were less punctual in August than the previous month.
Temporary speed restrictions were introduced between Ravenswood and Kangaroo Flat during August along track sections needing urgent repair.
The restrictions were lifted by the month's end. Track speed changes were implemented on another section, between Kyneton and Sunbury, in September.
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