Bins at key inner Melbourne train stations have been removed as part of a range of new security measures across the network.

Public Transport Victoria says the transparent bins - first introduced after the September 11, 2001 terror attacks - were removed over the weekend in response to the nation's new high terror alert level.

Stations believed to have lost bins include North Melbourne, Flinders Street, Southern Cross, Parliament, Melbourne Central, Flagstaff, Jolimont and Richmond.

PTV said in a statement operators were undertaking "a range" of precautionary security measures across the network, including the removal of rubbish bins at key locations.