Normal service has resumed on the Werribee and Williamstown lines after commuters had faced major delays when a truck struck a bridge.
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The truck struck the Napier Street bridge in Footscray on Thursday afternoon.
Metro Trains spokeswoman Pauline O'Connor said the incident occurred just after 5.40pm. There were delays of up to 25 minutes in both directions on the Werribee and Williamstown lines as a result.
The Napier Street rail bridge in Footscray suffers more hits from heavy vehicles than any other bridge in Melbourne and has been labelled "a time bomb" that, it is feared, will eventually result in the death of a pedestrian.
In May, the Maribyrnong City Council appealed to the Andrews government to fix the "extremely dangerous situation".
Williamstown/Werribee lines: Major delays in both directions due to a bridge hit at Footscray. See http://t.co/fE9E9Hyp10 for more info.— Metro Trains (@metrotrains) October 1, 2015
Train services on both the Sunbury and Pakenham lines were restored on Thursday evening after a faulty train and an accident had caused delays.
Earlier. outbound trains on the Sunbury line were experiencing delays of up to 30 minutes.
The Pakenham line had also experienced delays after a cyclist was hit by a train at Pakenham station after he rode his bike through the crossing.
Victoria Police spokeswoman Cath Allen said the accident happened just after 4pm.
"A male in his early 20s has been hit by a train at Pakenham railway station," Ms Allen said.
"It is believed he was riding his bike through the crossing when he was hit about 4.10pm."
Ms Allen said the man had non-life threatening injuries.
Victoria Ambulance spokeswoman Susannah Hicks said the man was taken to The Alfred hospital by road.
"He has significant head and leg injuries," Ms Hicks said.
Buses were used to replace trains in both directions between Berwick and Pakenham stations.