Bell Street is currently closed to traffic at the level crossing between High Street and St Georges Road after a boom gate was struck by a vehicle.
Motorists are being told to use Murray Road to avoid the closure.
Buses will replace trains on the Mernda line between Clifton Hill and Reservoir stations.
Train services will continue to operate between Flinders Street and Clifton Hill, and between Reservoir and Mernda, however delays are likely.
Authorised officers will be present to assist passengers changing between trains and buses.
Passengers are being advised to check station platform displays and listen for announcements, as well as allowing additional travel time.
