Coal-to-Liquid Fuel Energy Act of 2006 - Amends the Energy Policy Act of 2005 to include among the projects eligible for Department of Energy (DOE) loan guarantees large-scale coal-to-liquid fuel facilities that will produce at least 10,000 barrels a day of coal-to-liquid fuel.
Instructs the Secretary of Energy to establish a federal loan program for use by eligible recipients pay the federal share of the cost of obtaining services necessary for the planning, permitting, and construction of a coal-to-liquid fuel facility.
Amends the Energy Policy and Conservation Act to direct the Secretary to study and report to certain congressional committees on the feasibility and suitability of maintaining coal-to-liquid products in the Strategic Petroleum Reserve (SPR).
Authorizes the Secretary to acquire, place in storage, transport, or exchange coal-to-liquid products, not to exceed 20% of the total quantity of petroleum products in the SPR.
Amends the Internal Revenue Code to extend excise tax credits for certain alternative fuels and alternative fuel mixtures.