The location of exhaust stacks for the proposed Western Harbour Tunnel and Beaches Link toll road to Sydney's north east easily tops the list of public concerns about the project, government reports show.

The two scoping reports also show one of the options under consideration for the underground crossing of Sydney Harbour is an "immersed tube tunnel" sitting on top, or within the top layers, of softer sediments on the bottom of the harbour. The two other options involve digging twin tunnels to deeper depths below the harbour.

The cost of constructing the 14-kilometre tunnels linking Balgowlah in the city's north to Rozelle in the inner west have been estimated in leaked cabinet documents at $14 billion and will be partly funded from motorists paying tolls on northbound journeys of the Sydney Harbour Bridge and Harbour Tunnel.

The scoping reports show the state government has fielded more than 1000 comments from the public about the location and operation of ventilation stacks for the proposed tunnels. About 650 comments from the community related to the design of the project, such as tunnel entries and exits, 526 to public transport alternatives and 501 to potential property impacts such as compulsory acquisitions.