American Fuels Act of 2006

American Fuels Act of 2006 - Establishes in the Executive Office of the President the Office of Energy Security to oversee all federal energy security programs, including coordination of federal agency efforts to assist the United States in achieving full energy independence.

Amends the Internal Revenue Code to provide: (1) a tax credit for production of qualified flexible fuel motor vehicles, including allowance of the credit against the alternative minimum tax; and (2) an alternative fuel retail sales credit.

Amends the Clean Air Act to direct the Administrator of the Environmental Protection Agency to promulgate regulations to ensure that diesel sold or introduced into U.S. commerce, on an annual average basis, contains the applicable volume of alternative diesel fuel.

Requires such regulations to provide for the generation of an appropriate amount of credits by any person that refines, blends, or imports diesel containing a quantity of alternative diesel fuel greater than certain prescribed quantities.

Amends the Internal Revenue Code to extend the alcohol fuel mixture excise tax credit to cellulosic biomass ethanol.

Amends the Energy Policy Act of 1992 to include within the term alternative fueled vehicle a medium or heavy duty hybrid vehicle.

Sets a deadline by which: (1) any federal property with at least one fuel refueling station must include at least one alternative fuel refueling station; and (2) any alternative fuel refueling station on federally-owned property must permit full public access for the purpose of refueling using alternative fuel.

Amends federal transportation law to require that any bus purchased with funds from the Mass Transit Account of the Highway Trust Fund be a clean fuel bus.

Requires the Secretary of Defense to implement a program to evaluate the commercial and technical viability of advanced technologies for the production of alternative transportation fuels having applications for the Department of Defense.