Fisheries Restoration and Irrigation Mitigation Act of 2006

Fisheries Restoration and Irrigation Mitigation Act of 2006 - Amends the Fisheries Restoration and Irrigation Mitigation Act of 2000 to make the Fisheries Restoration and Irrigation Mitigation Program a pass-through program. Directs the Secretary of the Interior, acting through the Director of the U.S. Fish and Wildlife Service, to give priority to any project that has a total cost of less than $2.5 million (currently, $5 million). Makes development and implementation of projects on land or facilities owned by an Indian tribe nonreimbursable expenditures.

Requires: (1) any amounts provided by the Bonneville Power Administration directly or through a grant to another entity for a project carried out under the Program to be credited toward the non-federal share of project costs; and (2) the Secretary's report on projects under such Act to be made after partnering with local governmental entities and the states in the Pacific Ocean drainage area (Oregon, Washington, Montana, and Idaho).

Authorizes appropriations for the Act through FY2012. Sets forth a formula for determining the amounts that may be used for federal (including tribal) and state administrative expenses (based on the amount made available for the Program each fiscal year).