Indian Health Care Improvement Act Amendments of 2006

Indian Health Care Improvement Act Amendments of 2006 - Amends the Indian Health Care Improvement Act to revise requirements for health care programs and services for Indians, Indian tribes, tribal organizations, and urban Indian organizations.

Provides for: (1) enrollment of qualified Indians in the State Children's Health Insurance Program (SCHIP) under title XXI of the Social Security Act (SSA), as well as Medicare under SSA title XVIII and Medicaid under SSA title XIX (as under current law); and (2) related payments to Indian Health Programs and Urban Indian Organizations operating in the state.

Replaces the Urban Health Programs Branch with a Division of Urban Indian Health.

Directs the Secretary of Health and Human Services, acting through the Indian Health Service and Indian tribes and tribal organizations, to consolidate certain existing programs into a new program of comprehensive behavioral health, prevention, treatment, and aftercare for Indian tribes.

Establishes the National Bipartisan Indian Health Care Commission to: (1) establish a study committee to study the extent of Indian health services needs; (2) review and analyze the study committee's report; and (3) make recommendations to Congress regarding the delivery of federal health care services to Indians.

Reauthorizes the Indian Health Care Improvement Act through FY 2016.

Amends the Indian Self-Determination and Education Assistance Act to direct the Secretary to establish the Native American Health and Wellness Foundation.

Amends SSA title XIX (Medicaid) and XXI (SCHIP) to conform with this Act.