Infrastructure Victoria has advised the government that Bay West, somewhere between Werribee and Point Wilson, is the right choice for a future port, once container traffic outgrows capacity at the Port of Melbourne.

The port's container terminal would be built offshore - a four-kilometre-long industrial island connected with the mainland via a 1??-kilometre road and rail bridge that would radically reshape Port Phillip Bay.

New road and rail links would also be built across Melbourne Water's vast Western Treatment Plant, which is also a protected site for birdlife.

The other candidate, the Port of Hastings south-east of Melbourne, has been rejected owing to the estimated $5 billion cost of connecting it to Melbourne's rail network via the congested Pakenham-Cranbourne line and the environmental risk of ramping up shipping traffic in the ecologically sensitive Western Port.

Infrastructure Victoria argues Hastings should retain a smaller role among Victoria's ports, in the shipping of non-containerised goods such as cars.

It is believed a special subcommittee of the Andrews government will consider Infrastructure Victoria's advice on Thursday.

A spokesman would not confirm the decision but said the government had "now received Infrastructure Victoria's report into options on securing Victoria's future ports capacity".

"This report will be released in due course," he said.

However, the government is expected to welcome the choice.

Labor has indicated its preference for Bay West as the home for Melbourne's next major port for some years, including from opposition, arguing it would create jobs for Geelong and Melbourne's outer western suburbs.

This contrasts with the Coalition, which had already committed $110 million for environmental planning to develop the Port of Hastings before Labor won the 2014 election and cancelled the work.

But inner Melbourne will remain the heart of Melbourne's port activity for many years to come, despite the growing pressure this will place on the city's roads.

Infrastructure Victoria has assessed that the Port of Melbourne, Australia's busiest, should remain the focus of Victorian container trade for about 40 more years and will continue to grow over that time to about three times its current activity level.

Bay West would begin to take over once container traffic at the Port of Melbourne reached about 8 million shipping containers (TEU) a year. Infrastructure Victoria predicts traffic will reach this mark in about 2055.

The trigger of 8 million TEU is much lower than the port's new owners, the Lonsdale Consortium, believe is best.

The consortium, which paid $9.7 billion to lease the port for at least 50 years, said last month the port could handle 12 to 15 million containers a year if certain big changes are made to Melbourne's road and rail network.

Infrastructure Victoria estimates it will cost $6.1 billion-$6.4 billion to develop Bay West.

But Melbourne Water has issued a warning that costs could exceed this mark, given the future port's unquantified impacts on the neighbouring Western Treatment Plant.

Potential environmental impacts that could add extra costs include soil acidification and salinity, a rising water table inland of sewage treatment ponds and interference with the plant's effluent plume, Melbourne Water warned.

Indeed, the offshore terminal would be so large it could change the nature of Port Phillip Bay.

"A structure as big as the terminal island is likely to affect the entire bay and not just the area close to it," Melbourne Water said in a submission to Infrastructure Victoria.

A spokeswoman for Infrastructure Victoria said: "Infrastructure Victoria has delivered advice to the government on Victoria's future ports capacity. The advice covers the future need, timing and location of a second container port for Victoria."

Logistics expert Hermione Parsons said Bay West was the best choice, but argued the shift would need to happen in about 20 years time, not 40.

Dr Parsons, from Deakin University's Centre for Supply Chain and Logistics, said inner-city Melbourne would be overwhelmed with truck traffic by the time the Port of Melbourne handled 8 million containers a year.

The inability of larger vessels to safely pass beneath the West Gate Bridge would push most freight to Webb Dock, which has no rail connection.

"That's 230 trucks per hour, four trucks a minute, we think that is something the community is unlikely to support," Dr Parsons said.