The driver of the coach was trapped while others sustained minor injuries, the authorities said.
The four-car train hit the abandoned vehicle in Wollongong, located approximately 56 miles from Sydney, knocking the front coach onto its side and tilting the second.
The train, carrying 10 passengers and the driver, landed on the side behind the Kembla Grange railway station.
The driver was rescued by firefighters after being stuck for over an hour. The driver, along with four other injured persons on the vehicle, were taken to Wollongong Hospital.
The derailment took place at a time when the New South Wales (NSW) rail network is already affected by a strike over an alleged bid of privatisation, affecting up to 70 per cent of trains.
NSW Police Superintendent Craig Ireland said it would be a "massive recovery operation" and will cause disruptions to public transport to get that back on track.
"I was speaking to some of the railway workers on-site and when they see a train in that position, they immediately expect fatalities, so I think it is very fortunate no one was hurt," he told reporters.
A passenger who identified himself as Nick told Radio 2GB that he was lucky not to have been injured. “It was like being on a trampoline. Just bouncing up and down,” he said.
The Fire and Rescue team, in a statement, said they used extreme caution due to the potential live high-voltage electricity both above and below the train.
“Crews used special rescue equipment to extricate the 40-year-old train driver, who was suffering from back pain," they said.
Even though some trains between Wollongong and Waterfall are still running but buses are likely to replace trains in certain routes.
"A shuttle train service is operating in both directions between Albion Park and Kiama," NSW TrainLink South tweeted.
"Buses are on site and are operating a replacement service between Wollongong and Albion Park in both directions," it added.
The police have established a crime scene and are investigating the incident.
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