Ballarat commuters noticed on Tuesday rubbish bins had been removed from the city's main station.

The latest security measure comes after Prime Minister Tony Abbott raised the terrorism alert level to "high" earlier this month.

Bins have been removed from inner-Melbourne train stations including North Melbourne, Flinders Street, Southern Cross, Parliament, Melbourne Central, Flagstaff, Jolimont and Richmond.

A Public Transport Victoria spokeswoman said the rubbish bins were removed due to an increasing security alert.

She said it was one of many security measures being conducted across the public transport network.

"This is in line with the general increase in the security alert, not specifically because of any threat to public transport," the spokesperson said.

The spokeswoman said PTV could not comment on when and how many bins were removed, or any operational decisions regarding security measures.

It is unclear if or when the rubbish bins will ever returned to stations.

In the absence of bins, PTV has provided additional cleaning resources to the stations.

"Public transport customers are asked to be considerate and help to keep our trains tidy. Public transport operators are responsible for regular cleaning of trains and stations," the spokeswoman said.

Victoria Police and Ballarat City Council said they were not involved in the decision to remove the bins from train stations.