Platform 1 and 2 at Melbourne Central station were evacuated on Saturday afternoon with reports that a man had climbed onto a moving train and left a bag on the roof. The man has been taken to hospital for assessment.

On Twitter, witness Linton Wood posted a photograph of a blue sports bag on top of a train stopped at Parliament Station.

In another tweet, Mr Wood said: "It was pretty suss. He climbed up, left a bag and then sprinted off as we pulled up."

The City Loop section of the Cranbourne, Frankston, Pakenham, Sandringham, Hurstbridge and South Morang lines were closed as police searched the area.

Commuters were diverted to other platforms and told to catch their trains at Flinders Street and Richmond stations.

They were informed on speakers that the partial closure of the Loop was due to a "police operation", and that "unauthorised people" were running around in the tunnels.

Police searched the area, with fears the bag might contain a bomb.

A man was taken into custody by police and questioned on outstanding warrants. At about 4pm, normal train service resumed, with no injuries or other disruptions reported.

Police media spokeswoman Amelia Penhall said on Sunday that a 21-year-old Prahran man was taken to hospital for assessment.

She said he is expected to be charged on summons in relation to public nuisance and Transport Act offences.