A pay dispute has broken out between Metro Trains and the train drivers union over claims the company has underpaid 900 workers to the tune of more than $1 million in total.

The union is accusing Metro of breaching the Fair Work Act by failing to reimburse drivers who worked on a rostered day off and lodged a statement of claim in the Federal Court on Friday afternoon.

Metro and the RTBU are at loggerheads. Credit:Penny Stephens

It comes amid revelations that the global giant behind Metro is celebrating a 14 per cent revenue rise from Melbourne's rail network, despite the operator repeatedly failing to meet its performance targets.

Train drivers are eligible for an extra day off once every four weeks.