V/Line expects trains on the Bendigo line to resume this afternoon.
Trains are operating between Bendigo and Gisborne, with coaches between Gisborne and Melbourne's Southern Cross coach terminal in both directions.
Delays are expected due to heavy road traffic.
Coaches are now stopping at Riddells Creek and Clarkefield stations.
V/Line expects its first Bendigo train to leave Melbourne at 12.15pm from Southern Cross Station.
Between Sunbury and Gisborne only one of the two tracks is available for trains due to fire damage.
About 500 sleeps were damaged on the eastern line in a fire and trains will operate on the west line until repairs can be completed.
For updates, visit vline.com.au or follow@vline_bendigo on Twitter.