Health Equity and Justice Act of 2006

Health Equity and Justice Act of 2006 - Amends the Public Health Service Act to provide for: (1) establishment of the Robert T. Matsui Center for Cultural and Linguistic Competence in Healthcare; (2) programs to improve language access to health care for individuals with limited English proficiency; and (3) programs to improve health care for patient populations that have low functional health literacy.

Provides for the establishment of: (1) a national working group on workforce diversity; (2) a technical clearinghouse on health workforce diversity; (3) a health and healthcare disparities education program; and (4) an Advisory Committee on Health Professions Training for Diversity.

Requires federal health-related programs to: (1) require the collection of data on the race, ethnicity, and primary language of each applicant for and recipient of health-related assistance; and (2) analyze such data to detect racial and ethnic disparities in health and health care.

Renames the Office of Minority Health as the Office of Minority Health Disparity Elimination.

Requires the Indian Health Service (IHS) to be administered by an Assistant Secretary of Indian Health (in place of the Director of IHS), who shall report directly to the Secretary of Health and Human Services.

Requires four specified federal agencies to each establish an Office of Minority Health and Racial, Ethnic, and Primary Language Health Disparities Elimination. Directs the Secretary to establish: (1) an Office of Minority Health within the Centers for Medicare and Medicaid Services; and (2) an Office of Minority Affairs within the Office of the Commissioner of Food and Drugs.

Establishes the Interagency Working Group on Environmental Justice and the Federal Environmental Justice Advisory Committee.

Provides for grants to establish health empowerment zone programs in communities that disproportionately experience disparities in health status and health care.