Comprehensive Homeless Veterans Assistance and Prevention Act of 2006

Comprehensive Homeless Veterans Assistance and Prevention Act of 2006 - Reaffirms: (1) the national goal to end chronic homelessness among veterans within a decade of the enactment of the Homeless Veterans Comprehensive Assistance Act of 2001; and (2) encouraging all federal and local departments and agencies and public and private sector entities and organizations to work cooperatively to achieve such goal. Expresses the sense of Congress that federal agencies should cooperate more fully to address the veteran homelessness problem.

Extends various Department of Veterans Affairs (VA) programs and activities to assist homeless veterans, including: (1) grants for comprehensive homelessness services; (2) treatment and rehabilitation for seriously mentally ill and homeless veterans; (3) the transfer to VA homeless assistance programs of properties obtained through mortgage foreclosures; (4) a grant program for homeless veterans with special needs; and (5) the homeless veteran service provider technical assistance program.

Extends funding for rental assistance vouchers for a VA-supported housing program under the United States Housing Act of 1937.

Directs the Secretary of Veterans Affairs to provide financial assistance for supportive services for very low-income veteran families occupying permanent housing.