The Department of Transport released the final alignment for the two additional tracks through Footscray for the $4.3billion Regional Rail Link project, showing houses which will be demolished and those which will stay.

Twenty-five homes and 41 commercial properties will be demolished.

Residents began receiving phone calls and visits from department officers on Monday. But the messaging didn't go to plan. Some residents received letters saying their property would be acquired, followed by phone calls with conflicting information.

The tracks appear to have been shifted north to avoid demolishing houses in Short and Albert streets. The Salvation Army's hostel for the elderly in Buckley Street will not be touched. But houses along Buckley Street between Windsor Street and the Geelong Road overpass will be bulldozed.

The project was also referred to Planning Minister Justin Madden, who has 20 days to decide if an inquiry into the project's social, planning and environmental impacts is required. Albert Street resident Kim Hutchinson said the fight for a 'fair go' for those whose homes will be acquired would now begin in earnest. "Our next step is to ensure the planning minister makes an honest decision on what the environment effects statement is required to do and that an EES should be required for this project."

Victoria Street resident and carer Cathy Braniff lives on the northern side of the rail line in Middle Footscray. Her house will not be acquired, but she fears the rail line's impact during and after construction. Ms Braniff cares for the property's owner, Duc Tang, who has mental illness.

Rail link spokeswoman Ilsa Colson said a noise and vibration report formed part of the project's environment effects referral.