Tunnel digging on Melbourne's $11 billion Metro rail project has stopped as a dispute looms over costs.

The tunnel's two boring machines - nicknamed Joan and Meg - were shut down on Monday.

Tensions have been growing between the Victorian government and the consortium building the project over the cost, and mediators are now involved.

Cross Yarra Partnership was awarded the main tunnelling contract in 2017 after a tender process.

The consortium comprises companies John Holland, LendLease, Bouygues Construction and Capella Capital.

General view of a Metro tunnel construction site in Prahran. Credit: JAMES ROSS / AAPIMAGE

"Operational matters on the Metro Tunnel Project are a decision for Cross Yarra Partnership and Rail Projects Victoria," a government spokeswoman said in a statement.

"There is a contract in place to build the Metro Tunnel by 2025 and we expect them to deliver."

More on 7NEWS.com.au

Cross Yarra Partnership assured any queries regarding the project would be answered by Rail Projects Victoria.

"Rail Projects Victoria is in ongoing discussions with Cross Yarra Partnership on all aspects of the project and is focused on achieving the best outcomes as works progress," a spokesperson said.

"To date, Cross Yarra Partnership has not provided Rail Project Victoria with any specific detail of proposed changes to its tunnelling program."

Stoppage blame

Ensuring they remained committed to delivering the Metro Tunnel Project by 2025, Rail Project Victoria said both machines had travelled a combined 821 metres since launching earlier this year.

The construction union put the blame for the stoppage on engineering contractors John Holland.

The CFMEU said John Holland had suspended works, adding it was unknown who will wear the costs of the digging delays.

More than 40 workers from the tunnelling project have been sent to "training" by John Holland for the next few weeks, the union said.

It is unknown when they will return to work.

'Double standards'

"If the CFMEU shut down a project for no justifiable reason we would be fined tens of thousands of dollars," CFMEU Victoria secretary John Setka said.

"There are double standards when it comes to big business, in comparison to workers and their unions."

John Holland referred questions about the Metro project to the Cross Yarra Partnership.

Victorian Opposition Leader Michael O'Brien said the government had lost control of the state's major projects.

"This is a government which is so keen to get the headline it never meets a deadline."