The two billion dollar Melbourne-to-Geelong fast rail project included in the federal budget is an election eve "fantasy" with no money available for two years, the Victorian government says.

Treasurer Tim Pallas says no funds will flow for two years, despite Victorians being told building will begin in 18 months.

Only $50 million has been put aside in forward estimates for the project, which is in the Geelong region, where the Liberals hold ultra marginal seat, Corangamite.

Prime Minister Scott Morrison said on Wednesday money for the fast rail project is expected to flow once the business case is completed in about 18 months to two years.

“If we are in a position to start earlier we will,” he told ABC Melbourne radio.

Overall, Tuesday’s budget allocates $6.2 billion for new infrastructure projects in Victoria.

It also includes $1.1 billion for suburban roads upgrades and $700 million to duplicate rail tracks from South Geelong to Waurn Ponds.

Mr Morrison said the $700 million for the duplication will be spent over 10 years.

“It’s a big project. You can’t upgrade the Waurn Ponds line by going through a drive-through at McDonald’s, you’ve got to do the planning, you’ve got to get it done, you’ve got to work with the state government. I don’t think people expect these projects to be done overnight.”

Mr Pallas says the budget denied Victoria its fair share of infrastructure funds, with a 17.7 per cent share over the next five years, despite having more than 26 per cent of the population.

He also accused the Morrison government of continuing to hold onto $3 billion, originally earmarked for the dumped East West Link project.

The state government also said the budget confirms kinder funds will be cut from 2021 and has let hospital patients down with cuts to health.