UPDATE: Trains are resuming on the Mernda line between Clifton Hill and Flinders Street, following an earlier trespasser.
The Department of Transport said the trespasser has been apprehended by police.
The department has advised passengers to allow up to 30 minutes extra time for their journey across all lines as trains get back into position for the normal timetable.
EARLIER: The Mernda and train line has been suspended, with buses replacing trains between Clifton Hill and Flinders Street.
The Department of Transport said the suspension is due to trespassers on the tracks.
According to the department, other metropolitan lines are experiencing delays of up to 20 minutes for the same reason.
Passengers are being advised by the department to check station platform displays and listen for announcements.
Passengers should also allow extra time for their journey.
Services will resume as soon as it is safe to do so.
The department said the VicRoads signals team is monitoring conditions and will adjust traffic lights as needed to minimise congestion and assist with bus movements in the area.
Real-time traffic conditions are available online or via the VicTraffic mobile app.
Details: traffic.vicroads.vic.gov.au