Fuel Blend Reduction Act of 2006 - Amends the Clean Air Act (as amended by the Energy Policy Act of 2005) to: (1) require the Administrator of the Environmental Protection Agency (EPA), in coordination with the Secretary of Energy, to identify and publish in the Federal Register a list of five gasolines and diesel fuels to be used in state implementation plans (SIPs) (Federal Fuels List); (2) require an analysis of the ability of such listed fuels to reduce ozone emissions; (3) restrict the authority of the Administrator to approve fuels proposed in an SIP but not included on the Federal Fuels List; (4) require the Administrator, in consultation with the Secretary, to develop a federal-state fuel harmonization plan to be fully implemented by the states by December 31, 2008; and (5) revise requirements for the joint study of boutique fuels to require an analysis of the impact on ozone emissions and supply of a mandatory reduction to five in the number of approved fuel blends.