Environmental Justice Enforcement Act of 2006 - Amends the Civil Rights Act of 1964 to declare that discrimination based on disparate impact under federally assisted programs (including exclusion from participation and denial of benefits) is established only if a person aggrieved by discrimination on the basis of race, color, or national origin demonstrates that: (1) a covered entity has a policy or practice causing a disparate impact on that basis and fails to demonstrate that the challenged policy or practice is related to and necessary to achieve the nondiscriminatory goals of the program or activity alleged to have been operated in a discriminatory manner; or (2) a less discriminatory alternative policy or practice exists, but the covered entity refuses to adopt it.

Authorizes an aggrieved person to: (1) bring a civil action in federal or state court to enforce such person's rights; and (2) recover equitable relief, attorney's fees, and costs.

Makes the effective date of this Act retroactive to April 24, 2001.