Police declared the train station safe about 5.30pm after a bomb squad robot tugged at the white Windsor Smith bag that had been left on Collins Street outside a Sumo Salad cafe in Southern Cross Station.

Out tumbled a pair of black leather shoes.

Police had taped off the Collins Street entrance to the train station as well as a tram stop and blocked part of the street before the bomb squad arrived.

Workers from nearby offices were then evacuated and the intersection of Collins Street and Spencer Street cordoned off as pedestrians, workers and commuters were ordered away from the area.

Trains ran express through Southern Cross station but have now resumed running with only minor delays expected.

Traffic was blocked in both directions along Collins Street between Spencer Street and Harbour Esplanade in the Docklands.

V/Line passenger Kersty Whittaker said she had been shocked to find herself in the middle of a police operation.

"It was pretty scary," Ms Whittaker said.

"I've come up from Warrnambool and I'm not used to stuff like this," she said. "It feels like it's all linked to Paris and happening more now."

Another commuter said the response to the scare had been mixed.

"People wanted to know what was going on but some were rolling their eyes," she said. "You never really think it's going to happen where you are."