The fault, caused by overhead wires controlled by Metro, had the knock-on effect of trapping 160 passengers aboard a V/Line train from Traralgon for more than three hours in their carriages.

Metro Trains' emergency rail crew took several hours to fix the overhead power fault, that had occurred near Dandenong. More than 30 replacement buses were sent to stations affected on the two key rail lines.

Trains returned to normal service on Tuesday afternoon.

A V/Line spokeswoman, Catalina Filip, said the Traralgon train had left the Gippsland town at 4.36am this morning and had been unable to move forward around Dandenong because of Metro Trains' overhead fault.

The train was unable to move backward because of a stopped Metro train on the tracks.

Metro eventually cleared its train - but not before the V/Line passengers had waited more than three hours to get off the service safely.

They had been due to arrive at Flinders Street Station this morning just before 7am, but instead alighted at Hallam railway station after 10am.

Buses were sent to Cranbourne, Merinda Park and Lynbrook stations on the Cranbourne line, and to Berwick, Narre Warren and Hallam stations on the Pakenham line.

"Total disaster on the Pakenham and Cranbourne lines today," one commuter who wished to remain unnamed told Fairfax Media. "Queue at Berwick station at least 100 metres long. The best bit? Five customer service people standing at the top of the queue taking photos of us all standing in line."

The commuter said there had only been three replacement buses in one hour.

In Narre Warren, more than 200 passengers waited over half an hour for a bus replacement service.

At Carnegie station, waiting pains were also felt.