The giant tunnel boring machines digging the $11 billion Metro Tunnel project under central Melbourne will resume work on Thursday evening, but a deal is yet to be struck on who would help pay for a multibillion-dollar cost blowout.

The project's Cross Yarra Partnership consortium switched off two tunnelling machines on Monday morning, as the builders argued with the Andrews government over the blowout, which could be up to $3 billion.

The builders threatened to quit the project entirely unless the government agreed to chip in with the project's extra costs.

Premier Daniel Andrews responded in kind on Tuesday saying the dispute could end up in court if the consortium did not honour its contract with the state government.