As the Andrews government starts planning how trains will use the new tunnel, one option is for the Cranbourne-Pakenham services to skip South Yarra and Richmond and travel directly from Hawksburn to Domain, one of the five underground stations that will be built as part of $11 billion project.

If adopted, the realignment is likely to prove contentious given the number of people who use the two interchanges to get to work or sporting venues such as the MCG.

On one hand, it would require many commuters to find an alternative train service to reach their destinations, but, on the other, it could also free up some space at the ageing South Yarra Station, which users say is already stretched and in desperate need of refurbishment.

Stonnington Mayor Melina Sehr said she was not aware of the proposal to redirect the Cranbourne-Pakenham train lines, but added that bypassing South Yarra seemed "bizarre" given the extraordinary growth of residents who would require more trains to stop at the station in coming years, not less.

"And it doesn't change the issue, that the station needs an upgrade," she said.

Public Transport Users Association spokesman Daniel Bowen said if the government was planning such changes "they do need to explain it more clearly and justify why the decision is being made".

The government declined to comment when asked about the proposal on Saturday. However, Premier Daniel Andrews was keen to talk up the Metro Rail Project earlier in the week, when he revealed the underground rail line would travel beneath Swanston Street in a 10-metre-deep tunnel.

The long-awaited Metro Rail project involves creating a cross-city tunnel with five underground stations: Domain, CBD South, CBD North, Parkville and Arden. Once built, it will connect services from the Cranbourne-Pakenham lines (in the south-east) and the Sunbury line (in the north-west), thereby freeing up capacity in the City Loop to run more trains from other suburbs.

However, digging up the popular thoroughfare of Swanston Street is likely to cause years of disruption, forcing the government to create alternative tram routes in the city's west and potentially consider compensation for lost trade. It is also not yet clear how the project will be funded by the state, or to what extent the private sector would be willing to invest.

Asked how trains on the Cranbourne-Pakenham lines would connect to the new tunnel, a spokeswoman for the newly-formed Melbourne Metro Rail Authority replied: "Upon completion of Melbourne Metro, trains on the Cranbourne/Pakenham to Sunbury line will access the new Domain station via the Melbourne Metro tunnels. A new station at South Yarra is not part of the Melbourne Metro project, however that does not mean that improvements to South Yarra Station will not occur in the future."

Opposition transport spokesman David Hodgett warned Mr Andrews not to turn the Metro Rail into "another Myki or Desal Plant disaster".

"Melbourne is growing at almost 100,000 people per year and this is an incredibly important project that we have to get right," he said.