The price tag of Melbourne's Metro Rail project has come under question, amid government documents suggesting that constructing the tunnel deeper underground to avoid severely disrupting the city could cost an extra $600 million.

In a surprise move last week, the Andrews government announced it would dump plans to dig a shallow rail tunnel only 10 metres beneath Swanston Street, and instead go as far as placing parts of the project almost 40 metres underground.

Premier Daniel Andrews insisted the new construction plans would end up saving money, while Transport Minister Jacinta Allan described the costs as being "comparable" for taxpayers compared with the design chosen earlier this year.

However a ministerial briefing suggests otherwise, pointing out that the shallow alignment would be better for passengers and would also save hundreds of millions of dollars.