Within weeks, rolling strikes spanning 24 to 48 hours could hit every regional train line, if up to 600 drivers, station staff and train controllers vote to down tools.

The Rail, Tram and Bus Union (RTBU) lodged an application to take protected industrial action at the Fair Work Commission on Tuesday afternoon, which must be approved by a majority of members for the strike to go ahead.

The union is considering first targeting the Geelong and Warrnambool lines, followed by Ballarat, Maryborough, Bendigo, Seymour, Shepparton and Gippsland.

Commuters on many of these lines already face chronic overcrowding and unreliable services, and have endured many months of bus replacement services, due to the state government's works on major transport projects.

The union also plans to have one-hour work bans, which would lead to delays and cancellations, incurring fines for V/Line.

V/Line workers are calling for a 6 per cent annual pay rise over three years, while the state government-owned rail operator has put 2 per cent on the table. V/Line's enterprise bargaining agreement expired in June this year.

Secretary of the union's locomotive division, Marc Marotta, warned of a "long and bitter struggle", accusing V/Line of pursuing a "scorched earth policy towards employees".

"We've had something in the order of 15 or 16 meetings and we are getting nowhere," Mr Marotta said. "We are being told rubbish in the meetings."

The union said that V/Line was removing driver training provisions, an eight-hout shift guarantee, public holiday loadings and other penalties in documents lodged with the Fair Work Commission.

"They are looking to strip away nearly every condition that workers have got at V/Line," he said.

A V/Line spokesman said that any offer would need to be consistent with government wages policy.

"We'll continue to negotiate in good faith with our workers' representatives about the new V/Line operations workplace agreement," he said.

In a separate matter, the union's secretary Luba Grigorovitch has launched legal action against Metro Trains in the Federal Court to clear the way for Metro workers to strike.

Metro has argued the union failed to comply with court orders, which meant that Metro staff could not legally take strike action.

The union is now seeking to remove those court orders in the Federal Court, so it can launch strikes on the suburban rail network. The case has been adjourned until November 6.

The union is also running a public campaign against Metro, with about 200 Metro workers gathering on the steps of Flinders Street Station last week amid the bitter pay dispute.

About 60,000 leaflets with the words "Profit Express" will soon be distributed to commuters at train stations across the city.

The leaflets feature a caricature of Metro as an overweight, money hungry train operator and claim Metro profits by "screwing workers" and "screwing commuters".

A Metro spokesman said the company put forward a pay offer of 3.5 per cent a year over four years, which included improved trauma leave, flexible working conditions and an increase in parental leave from 12 to 14 weeks.

"We have consistently maintained that a new deal can be reached around the negotiating table without disrupting the travelling public," the spokesman said.

The Age