Melbourne rail workers are threatening to shut down the city's trains for up to two days after negotiations over a pay deal broke down.

Key points: Workers rejected 2 pc offer over 4 years, instead pushing for 17 pc rise

Workers rejected 2 pc offer over 4 years, instead pushing for 17 pc rise Union filed for protected industrial action

Union filed for protected industrial action Possible strike 4-6 weeks away

The Rail, Tram and Bus Union (RTBU) lodged an application for protected industrial action after rejecting an offer of 2 per cent over four years from Metro Trains.

The pay deal covers infrastructure staff, such as track workers, signallers and administration staff.

The union, which was pushing for a 17 per cent pay rise, described them as being the "backbone" of the railway.

RTBU secretary Luba Grigorovitch said negotiations with Metro broke down after an "insulting and unacceptable" offer was tabled on Tuesday.

She called for a range of industrial action, including strikes of between one and 48 hours, but any action would be four to six weeks away.

"We will continue to negotiate in good faith, but in the absence of a fair and reasonable agreement presented by Metro in the coming weeks, we'd have no choice but to take the industrial action," Ms Grigorovitch said.

"Our members are not willing to entertain this any longer.

"Their agreement expired nine months ago and the offer that Metro put forward was terrible: a 2 per cent wage increase over four years and a number of conditions stripped away."

Parties urged to continue negotiations

Public Transport Minister Jacinta Allan said she was confident the strikes would not happen.

She said the union was one of three negotiating with Metro, adding its members were not representative of the entire workforce.

"There are many steps and many, many weeks to go through before there's even the potential of any action being taken," she said.

"The best way to get these matters resolved is through negotiations in good faith and that's certainly what the Government is urging on both parties."

Ms Grigorovitch said the "ball is in Metro's court".

"They need to put forward an offer that is actually acceptable to the membership," Ms Grigorovitch said.

"The last thing we want to do is take industrial action."

Opposition MP David Hodgett said the Government should stand up to the rail union.

"Commuters are fed up with being held to ransom during this strike action," he said.

"Daniel Andrews and Jacinta Allen need to stand up to that union and not cave into a massive 17 per cent pay rise."

Striking train drivers shut down Melbourne's trains several times last year before their pay deal was settled.

Minister facing 'many challenges'

But Public Transport Users Association spokesman Daniel Bowen said parts of Melbourne's train network might have to shut down if key staff take industrial action.

"If key workers go on strike, there's the potential for the train system to stop running," he said.

"That's clearly going to cause a huge disruption, not just on the train line but also across Melbourne due to flow-on effects.

"We'd appeal to the union and the Government and the operator to make sure this is resolved quickly and peacefully without resorting to industrial action."

The strike threat has put more pressure Ms Allan, who is also grappling with V/Line's woes and fierce backlash over the Government's plan to build "sky rail" in Melbourne's south-east to remove level crossings.

Mr Bowen said Ms Allan was facing many challenges.

"She's going to have to lift her game I think, and face up to the issues in industrial relations, sky rail, V/Line, there are a lot of problems to fix," he said.