Corporate Average Fuel Economy Reform Act of 2006 - Amends federal transportation law to direct the Secretary of Transportation to prescribe minimum corporate average fuel economy (CAFE) standards for passenger automobiles, including standards that are based on one or more vehicle attributes that relate to fuel economy. Requires the Secretary of Transportation, when deciding maximum feasible average fuel economy for passenger automobiles, to consider (in addition to current considerations) motor vehicle safety, emissions, and the need of the United States to reduce its dependence on oil for transportation.

Solicits comment from the Department of Energy (DOE) (currently) and the Environmental Protection Agency (EPA) before the Secretary issues a notice for a proposed or amended CAFE standard.

Allows manufacturers to earn credits which may be applied to any five (currently, three) consecutive model years after the year in which they were earned if the average fuel economy of passenger automobiles manufactured by a manufacturer in a particular model year exceeds an applicable established average fuel economy standard. Permits trading credits between passenger-automobile production and non-passenger-automobile production.

Requires civil penalties assessed by the Secretary or by a Court against a person who violates CAFE standards to be credited to a Department of Transportation (DOT) account and made available to carry out a program of research and development into fuel saving automotive technologies and to support the CAFE program.