Homeowners Preservation of Equity Act of 2006 - Directs the Secretary of the Treasury, in consultation with federal banking agencies, the National Credit Union Administration, and the appropriate state bank supervisors of each state contained in whole or in part in the GO Zone (as defined by the Internal Revenue Code), to establish a program to provide temporary emergency mortgage payments on behalf of an eligible individual whose principal residence was significantly damaged or made uninhabitable by Hurricane Katrina or related flooding.