More than 1800 damaged sleepers and 180 metres of railway track is being replaced after Wednesday's train derailments at Barnawartha.
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About 60 workers from a range of agencies had cleared the last of the trains, carriages, containers and wagons spread over 1.7 kilometres by Friday afternoon.
A famous Ghan fleet locomotive shunted the final freight wagons from Barnawartha on Friday afternoon.
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The main point of access to and from the town, near the Hume Highway, reopened.
While the scene has been cleared, Australian Rail Track Corporation spokesman Peter Winder said further action was needed.
"Work is now under way to replace more than 1800 damaged sleepers and more than 180 metres of damaged rail," he said.
"While repairs are under way, timing for the line to reopen is not yet confirmed."
Australian Transport Safety Bureau staff confirmed 17 V/Line passengers and three crew were assessed after the train was struck by freight containers.