Zero Tolerance for Veterans Homelessness Act of 2012

Zero Tolerance for Veterans Homelessness Act of 2012 - Allows grants made by the Secretary of Veterans Affairs (VA) for homeless veterans' comprehensive services programs (outreach, rehabilitation, vocational counseling, and transitional housing assistance) to be used for the construction of new facilities. Prohibits the Secretary from denying applications for such grants solely on the basis that the grant entity proposes to use funding from other private or public sources, as long as such entity demonstrates that a private nonprofit organization will provide project oversight and site control. Requires the Secretary to: (1) study matters relating to the method used to make per diem payments to grant recipients, (2) develop more effective and efficient procedures for fiscal control and fund accounting by grant recipients, and (3) develop a more effective and efficient method for adequately reimbursing grant recipients for services furnished to homeless veterans.

Amends the Department of Housing and Urban Development Act to establish in the Department of Housing and Development (HUD) a Special Assistant for Veterans Affairs.

Directs the Secretary to submit to Congress a comprehensive plan to end homelessness among veterans. Requires the plan to include consideration of the circumstances and requirements unique to veterans located in rural areas.