Sunbury line trains were suspended for an hour on Tuesday morning due to a police operation in St Albans.
The operation forced the closure of the line between Sunshine and Watergardens.
Six Metro services were cancelled and a V/Line train from Bendigo was stopped at Sunbury station while police carried out the operation.
The incident affected hundreds of passengers.
A passenger on the Bendigo train said carriages were “very full”.
A Metro Trains spokeswoman said buses replaced trains during the operation.
Services resumed just after 10am and Metro expected delays of up to 15 minutes while the timetable was restored.
V/Line Bendigo said the 10.15am and 11.36am Bendigo to Southern Cross Station services were cancelled and replaced by buses.
Police confirmed there was an operation at the station but would not comment further.
Fairfax Media believes the operation was caused by a person threatening self-harm.
This is the second time in as many days that services have stalled on the Sunbury line.
On Sunday, about 150 passengers were stranded for about 90 minutes after a power line came down on tracks close to Keilor Plains station.
