A half-billion dollar plan to run trains every two minutes along Melbourne's busiest railway line using cutting-edge high-speed signalling is in doubt because of fears the technology will not work on Melbourne's 19th-century rail network.

The government and the consortium behind the project want to lock in contracts by the end of this month, despite alarm from rail experts at the Transport Department that the complex technology installation could lead to a myki-style cost blowout.

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

The move to "21st-century high-capacity signalling" is one of the key features of the Napthine government's $2 billion-$2.5 billion upgrade of the Cranbourne-Pakenham rail corridor, which is used by about 70,000 passengers each weekday.

The rail line is shared by Metro, V/Line and freight trains and is among the worst for peak-hour overcrowding in Melbourne.