National Fund for Excellence in American Indian Education Amendments Act of 2006 - Amends the Indian Self-Determination and Education Assistance Act with respect to the National Fund for Excellence in American Indian Education (Foundation). Requires the Foundation Board to appoint a chief operating officer for the Foundation separate from the Secretary of the Interior (who currently acts as chief operating officer).
Places limitations on the administrative costs of the Foundation. Authorizes appropriations for FY2007-FY2009. Authorizes the Secretary to provide funds to pay the operating expenses of the Foundation.