A police operation in the early peak period caused confusion, causing the passengers to be detained after the train line was closed.
All trains heading for North Melbourne Station on the Craigieburn,Sunbury,Upfield,Werribee and Williamstown lines are suspended.
The cause of the incident was that the station was found to have a suspicious package, and police are investigating, causing major delays in all the affected routes.
"the Victoria State Police Department is currently conducting a security check in North Melbourne because of suspicious items," Metro Trains said.
"while the investigation is still under way, trains along the railway have ceased to operate and the crowd at the station has been evacuated."
The chaos left passengers stranded on the platform, placing a heavy burden on the urban bus network and causing bus delays.
Commuters say the train came back the way they came, and an ambulance arrived at South Kensington Station.
The Victoria State Police Department said the station had been evacuated and the train did not stop at the station just in case.
