Department of Health and Human Services Tribal Self-Governance Amendments Act of 2004

Department of Health and Human Services Tribal Self-Governance Amendments Act of 2004 - (Sec. 2) Amends the Indian Self-Determination and Education Assistance Act to provide for further self-governance by Indian tribes.

Establishes a five-year project to demonstrate the effectiveness of tribal operation of certain programs currently operated by the Department of Health and Human Services (HHS).

Entitles up to 50 eligible Indian tribes to participate in the demonstration project; but authorizes the Secretary of HHS, if more than 50 request participation, to select additional tribes to participate. Makes a tribe eligible for a project only if it is party to a tribal self-governance compact or a funding agreement relating to certain Federal programs. Directs the Secretary to establish a program to award planning and negotiation grants to eligible tribes, but states that receipt of such a grant is not a requirement for project participation.

Sets forth requirements for compacts and funding agreements.

Makes eligible for inclusion in a funding agreement the following programs: (1) grants for older Native Americans; (2) tribal temporary assistance for needy families; (3) Low-Income Home Energy Assistance; (4) Community Services Block Grant; (5) Child Care and Development Fund; (6) native employment works; (7) Head Start; (8) child welfare services; (9) promoting safe and stable families; (10) family violence prevention grants for battered women's shelters; (11) targeted capacity expansion, related to substance abuse and mental health services; (12) mental health and substance abuse block grant; and (13) community health center grants.

Authorizes the Secretary to identify up to six additional programs annually for inclusion in the demonstration project, including: (1) all other programs in which Indian tribes are eligible to participate, or for which Indians are eligible beneficiaries; and (2) competitive grants for which an Indian tribe receives an individual or cooperative award, upon agreement to such grant restrictions regarding program redesign and budget reallocation.

Prescribes requirements for: (1) contents of funding agreements; (2) transfer of funds; (3) waivers for redesign, consolidation, and reallocation; (4) procedures in cases of inability to agree on a compact or funding agreement; and (5) reports.

Authorizes appropriations.