The state government is facing a hefty compensation bill after a business displaced by the Regional Rail Link launched a legal bid to recoup millions of dollars in unanticipated costs.

Logistics firm Container Forwarding Services was forced to leave its rented premises in Joseph Road, Footscray, to make way for the regional rail link and a new routing of the Werribee metro line.

Following the government's compulsory acquisition of the land in May 2011, the company received compensation of $534,000 and moved to Tottenham.

But the company is claiming the six-kilometre move has generated at least $2.57 million in unanticipated costs.

Company director David Young is claiming the rent for the new facility is $257,340 more expensive and the longer travel distance has added $307,739 in transport expenses.

Another $1.72 million is being sought as ''reasonable disturbance costs'' and $147,000 to buy a forklift and pay a project manager to run the operation. Mr Young declined to comment because the matter is before the Supreme Court.

The lawsuit comes as the Regional Rail Link Authority continues to negotiate compensation settlements for a number of businesses in the Footscray area forced to move as a result of the expansion of the network.

''Aside from the claims still being resolved, Regional Rail Link Authority is not aware of any lawsuits relating to land acquisition in Footscray as part of the RRL project,'' a spokesman said.

The authority was recently blasted by the Auditor-General for failing to disclose information about the cost of the 40-kilometre project. The budget of the RRL has soared, from $4.3 billion to $5.5 billion in March 2011, only to be revised downwards to $4.8 billion.

Transport Minister Terry Mulder did not respond to a request for comment.

cvedelago@fairfaxmedia.com.au

Twitter: @chrisvedelago