Metro Trains is being probed by the public transport watchdog over complaints about trains changing destinations while commuters are still on board.

The probe was revealed in the Public Transport Ombudsman's annual report, released on Tuesday, which found reliability and punctuality copped the most complaints from commuters.

In a bid to meet its punctuality targets, Melbourne's rail service sometimes changes the destination of a train after it departs Southern Cross and arrives at Flinders Street - a practice known as transposing services.

This is done on incoming trains arriving late at Flinders Street - where the train is scheduled to wait for a few minutes as drivers change over - to avoid delays flowing onto other lines.

Public Transport Users Association spokesman Daniel Bowen said transposal services should be kept to a minimum, and called on Metro to switch the train's destination before it departs Southern Cross, rather than waiting until commuters are on board.