Tunnelling on the $6.7 billion West Gate Tunnel has been delayed due to the discovery of soil contaminated with a chemical that shut down the Fiskville CFA training college.

The project is now facing potential cost blowouts, as the state government, joint-venture builders CPB Contractors and John Holland, and Transurban scramble to find a way to store, transport and clean the contaminated soil found at the site in Melbourne's industrial west.

Chemicals including asbestos and PFAS, which shutdown the CFA college, have been detected in the ground.

Two 450-tonne tunnel boring machines were lowered at a launch site in Yarraville in August, but sources say they have not moved due to the contaminated soil issue.