Coal-to-Liquid Fuel Promotion 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 facilities that use a feedstock, the majority of which is domestic coal resources, to produce at least 10,000 barrels a day of liquid transportation fuel.
Instructs the Secretary of Energy (Secretary) to establish a federal loan program for coal-to-liquid facilities.
Directs the Secretary to promulgate regulations to support the development of coal-to-liquid manufacturing facilities and associated infrastructure on DOE and other federal lands, including military bases and military installations closed or realigned under the defense base closure and realignment.
Authorizes the Secretary to construct storage facilities: (1) in the vicinity of pipeline infrastructure and at least one military base; but (2) outside the boundaries of any state on the coast of the Gulf of Mexico.
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 Strategic Petroleum Reserve.
Authorizes appropriations for the Air Force Research Laboratory to continue support efforts to test, qualify, and procure synthetic fuels developed from coal for aviation jet use.
Amends federal law governing Armed Forces fuel procurement to authorize the Secretary of Defense to enter into agreements with private companies to develop and operate coal-to-liquid facilities on or near military installations.