Indian Trust Payment Equity Act of 2003

Indian Trust Payment Equity Act of 2003 - Requires the Secretary of the Interior for each of FY 2004 through 2008 to use $2 billion of the amounts in the Indian Trust Payment Equity Fund established by this Act to provide payments to Indian tribes for amounts owed by the United States to individual Indian money account holders as a result of mismanagement of the individual Indian money fund.

Authorizes the Secretary: (1) to enter into a contract with an Indian tribe under the Indian Self-Determination and Education Assistance Act, or amend such a contract, to provide funds to the Indian tribe from the Fund to assist it in performing audits of individual Indian money accounts in accordance with generally accepted Federal accounting standards; and (2) if the account holder accepts the results of an audit, to use amounts in the Fund as partial payment until a full accounting is satisfied.

Provides that nothing in this Act: (1) negates or otherwise affects the requirement of the Department of the Interior to complete the accounting; or (2) constitutes a settlement regarding any individual Indian money account or any civil action to compel an accounting and payment of amounts owed to such account holders.

Establishes the Indian Trust Payment Equity Fund in the Treasury to be used to carry out this Act, consisting of amounts appropriated under this Act.