The union representing Metro Trains staff is refusing to agree to plans to run trains all night on Fridays and Saturdays from January 1, putting a key Labor election promise in jeopardy, leaked correspondence reveals.

The threat to ruin the Andrews government's new year's party is the latest standoff in an increasingly bitter pay negotiation that also appears set to shut down Melbourne's rail system for four hours on Friday.

Metro has offered the Rail, Tram and Bus Union a one-off 3 per cent pay rise, on top of a 14 per cent increase over four years, if the union helps to implement Homesafe, the government's promised 24-hour public transport trial next year.

But Melbourne's rail operator has tied the 3 per cent carrot to a string of other significant changes it wants to make to staff working conditions, particularly for train drivers, which the union has firmly rejected.

These include changes to public holiday penalty rates and an end to restrictions that prevent drivers from running on the same line repetitively.

Metro says the changes are crucial if Melbourne's trains are to cope as demand grows.

The jockeying between Metro and the union over 24-hour trains is revealed in a letter union secretary Luba Grigorovitch sent to Metro chief executive Andrew Lezala on Tuesday, September 1.

The letter reveals that Ms Grigorovitch offered to suspend all industrial action if Metro accepted the union's "alternative proposition" on driver rostering and training.

But the offer was withdrawn, the letter reveals, after Metro sought to lock the union into ruling out taking any industrial action for 21 days.

Ms Grigorovitch said she could not agree to Homesafe because Metro had given no details about how it will be run.

"I make no apology that the RTBU will continue to fight changes that Metro are trying to sneak through. We do this in the interest of public safety," she said.

"Items that Metro are trying to force on members such as less training for drivers and repetitive running have proven to lead to complacency which is unsafe for the travelling public."

Metro said late on Monday that negotiations with the union were "at an impasse".

The company will attempt to have Friday's four-hour stoppage cancelled by the Fair Work Commission on Wednesday, on the grounds that it is a threat to public health.

The Andrews Government announced on Tuesday night that it would join Metro's application.

"This is not a decision we have taken lightly. As the Labor Party, we believe in the right of unions to take lawful industrial action," Public Transport Minister Jacinta Allan said in a statement.

"But the right to take industrial action comes with great responsibility - responsibility to the public who it affects, as well as responsibility to union members."

The union has timed the stoppage to avoid peak hour, but it will still create chaos given Melbourne's rail system carries about 680,000 people each weekday.

Metro says growing rail patronage explains why it must change train driver rostering arrangements.

The operator plans to split Melbourne's railway network into five discrete groups, with minimal crossover points, to end the situation where a disruption on one line spills onto others and causes commuter chaos.

Under the plan, most drivers would be restricted to one of the five groups and would not need to be trained to operate on all lines.

The union's locomotive division secretary, Marc Marotta, has slammed the plan as "a deskilling program of train drivers" that will open the door to a new grade of lower-paid staff, in a report to members seen by The Age.

The report details 13 conditions Metro is seeking agreement on, all of which the union has refused.

Heading the list of rejected conditions is "sectorised running" - limiting train drivers to one part of the network - and Labor's $83.6 million 12-month trial of 24-hour public transport on weekends.