American Indian Trust Fund Management Reform Act Amendments Act of 2003

American Indian Trust Fund Management Reform Act Amendments Act of 2003 - Amends the American Indian Trust Fund Management Reform Act of 1994 to revise the accounting duties of the Secretary of the Interior with respect to the daily and annual balances of all monies or proceeds derived from trust assets and funds held in trust by the United States for the benefit of an Indian tribe or an individual Indian. Requires an annual audit only for accounts with over $1,000 in trust funds, but for accounts with less than $1,000, only statistical sampling audit procedures of all such accounts grouped separately. Specifies minimum additional responsibilities of the Secretary.

Allows an Indian tribe to use authority granted to the tribe under the Indian Self-Determination and Education Assistance Act to manage Indian trust funds and trust assets without terminating the trust responsibility of the Secretary or the trust status of the funds and assets.

Replaces the current Office of Special Trustee for American Indians with a Deputy Secretary of the Interior for Indian Affairs to: (1) oversee the Bureau of Indian Affairs; (2) carry out all duties currently assigned to the Assistant Secretary for Indian Affairs; and (3) oversee all Indian trust fund and trust asset matters, and consult with Indian tribes and individual trust asset and trust fund account holders.

Establishes within the Office of the Secretary the Office of Trust Reform Implementation and Oversight, headed by such Deputy Secretary, to supervise and direct day-to-day activities concerning such assets or funds, including providing accurate inventories, revenue postings, monthly statements, and annual audits.

Establishes a Commission for Review of Indian Trust Fund Management Responsibilities to assess the fiduciary and management responsibilities of the Federal Government with respect to Indian tribes and individual Indian beneficiaries.