Millions of Victorians have been paying a hidden public transport fee for more than a year to help fund the $34.5 billion Suburban Rail Loop.

The levy to help bankroll the Suburban Rail Loop was exposed by the Victorian Auditor-General, who also warned the project was at risk of running late and over budget.

The levy was exposed by the Victorian Auditor-General on Wednesday, which also warned the project was at risk of running late and over budget.