Boutique Fuel Reduction Act of 2006

Boutique Fuel Reduction Act of 2006 - Amends the Clean Air Act to add as "extreme and unusual circumstances that prevent the distribution of an adequate supply of fuel or fuel additives to consumers" under which the Administrator of the Environmental Protection Agency (EPA) may temporarily waive a control or prohibition on the use of a fuel or fuel additive circumstances that are the result of unexpected problems with equipment necessary for transportation and delivery of fuel or fuel additives.

States that EPA shall have no authority, when considering a state implementation plan (SIP) or SIP revision, to approve any fuel included in such plan or revision if the effect of such approval increases the total number of fuels set forth on the published list of approved fuels (currently EPA does not have the authority to approve a fuel if it increases the total number of fuels approved as of September 1, 2004, in all SIPs).

Requires notice and opportunity for comment before EPA removes a fuel from the list. Requires EPA to remove a fuel from the list if such fuel has ceased to be included in an SIP or is identical to a federal fuel control or prohibition. Repeals provisions prohibiting EPA from reducing the total number of authorized fuels. Requires EPA to publish a revised list reflecting the reduction in the number of fuels.

Amends the Energy Policy Act of 2005 to change the deadline for a report by the Administrator and the Secretary of Energy concerning motor vehicle fuels (currently, June 1, 2008) to the earlier of: (1) nine months after the date of enactment of this Act; or (2) June 1, 2008.