The Napthine government's rushed re-routing of the new underground rail line to Fishermans Bend is disrupting plans for billions of dollars of residential and commercial projects in Docklands and South Melbourne.

Developers and landowners along the proposed route between Southern Cross station and South Yarra have been notified – in some cases on the basis of strict secrecy – that the $11 billion rail route may affect major new high-rise developments, whose foundations sink deep underground.

Fishermans Bend.

Among them are Lend Lease's $1.5 billion Batman's Hill and a planned high rise tower at Normanby Road, South Melbourne, near the proposed Montague rail station. The station is designed to serve the 80,000 residents at the Fishermans Bend redevelopment.

Project architect Kim Lowman confirmed the discussions with government. He said planning approval appeared to have been delayed because of the tower's proximity to the tunnel and proposed Montague station site.