Native Hawaiian Government Reorganization Act of 2006

Native Hawaiian Government Reorganization Act of 2006 - Establishes the U.S. Office for Native Hawaiian Relations within the Office of the Secretary of the Interior.

Establishes the Native Hawaiian Interagency Coordinating Group.

Recognizes the right of the Native Hawaiian people to reorganize the single Native Hawaiian governing entity to provide for their common welfare and to adopt appropriate organic governing documents.

Establishes a Commission to: (1) prepare and maintain a roll of the adult members of the Native Hawaiian community who elect to participate in such reorganization; and (2) certify that the adult members of the Native Hawaiian community proposed for inclusion on the roll meet the definition of Native Hawaiian.

Outlines the process for the reorganization, which includes forming a Native Hawaiian Interim Governing Council.

Reaffirms the special political and legal relationship between the United States and the Native Hawaiian governing entity upon certification required by the Secretary regarding the organic governing documents and the election of the entity's officers. Extends federal recognition to the governing entity as the representative governing body of the Native Hawaiian people.

Authorizes the United States, upon the reaffirmation of such political and legal relationship, together with the state of Hawaii, to enter into negotiations with the governing entity to lead to an agreement addressing specified matters, including the transfer of lands, natural resources, and other assets, and the protection of existing rights related to such lands or resources.