Replacement buses on the Shepparton line have left passengers waiting more than an hour before they even leave the station.
Buses are replacing trains between Southern Cross, Seymour and Shepparton until Saturday, April 2.
Buses will then replace trains between Seymour and Shepparton until the last service on Thursday, April 6.
Commuters have reported waiting up to an hour on coaches while they are filled, adding significant time to their journeys.
From April 2 to April 6, coaches will depart Shepparton up to 35 minutes earlier than usual train times to ensure connection with trains at Seymour.
A temporary timetable will be available from the V/Line website.
The works include signalling work, commissioning, safety testing and driver training.
Passengers can check the PTV app or website at ptv.vic.gov.au before travelling and allow 60 minutes extra for their journey.