A federal budget injection of more than $850 million for the Melbourne Metro Rail tunnel should go towards building an underground station at South Yarra, Victoria's Opposition says.

The Melbourne Metro will pass just metres beneath South Yarra station but will not connect with it, even though it is used by more passengers than any other railway station outside the CBD.

"Almost everyone agrees Melbourne needs an extra north-south rail link through the city, but we need to make sure we get it right," opposition public transport spokesman David Hodgett said.

"Not including an interchange station at South Yarra, the biggest station outside of the city, is poor planning and short-sighted."