More than 300 V/Line staff are currently in isolation, with five confirmed coronavirus cases among the workforce as of late on Sunday night.

Both drivers and operational staff have tested positive.

The result will mean coaches will replace almost all regional trains, with only two morning peak services on the Ballarat and Bendigo lines, as well as a full service on the Seymour line.

The two Ballarat trains departed before 7am.

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Coaches will run at a 30-minute frequency during the peak on the Ballarat line and 60 minutes across the rest of the day, according to V/Line.

They are expected to depart 25 minutes before usual train times and customers should allow an extra 90 minutes for their journey.

In a statement, the Department of Transport said it had plans in place should such an incident occur, both in terms of safety and also maintaining a transport service.

See all the current exposure sites here.

"V/Line's COVIDSafe plan has a number of general contingency plans for different types of service disruptions, allowing it to modify services and put alternate transport options in place quickly whenever services are disrupted, including due to a COVID-19 exposure," the statement read.

"A number of controls have been in place during the coronavirus pandemic to keep drivers and passengers safe, including physical distancing requirements and measures in common areas, mandated mask wearing, QR codes, additional cleaning, temperature testing for staff, encouraging good hygiene practices, as well as regular communications with our staff about working in a COVID safe environment.

"V/Line and the Department of Transport are working closely with the Department of Health to support the V/Line staff and we are exercising an abundance of caution in the interest of our crews and passengers."

See the V/Line website for the latest information.