Spent Nuclear Fuel Control and Accounting Act of 2006

Spent Nuclear Fuel Control and Accounting Act of 2006 - Amends the Nuclear Waste Policy Act of 1982 to direct the Nuclear Regulatory Commission (NRC) to promulgate regulations requiring: (1) each civilian nuclear power reactor to report a detailed record of each individual spent fuel rod, and each fragment of a spent fuel rod, that results from the loading or dismantling of a fuel assembly; and (2) annual inspections to determine the compliance of the civilian nuclear power reactor with NRC regulations relating to the material control and accounting of spent nuclear fuel.

Requires the NRC to develop and make available to each civilian nuclear power reactor guidance that describes: (1) best management practices for storing individual fuel rods and fragments; and (2) suitable annual inventory practices.

Directs the NRC to develop an electronic data management and waste tracking system to: (1) store and access the records of each civilian nuclear power reactor; and (2) track the location of spent nuclear fuel, including individual rods and fragments.

Instructs the NRC to: (1) develop a detailed manifest form for the onsite transportation of spent fuel that indicates whether the package containing the spent fuel contains individual rods or fragments; and (2) promulgate regulations requiring each civilian nuclear power reactor to provide the NRC a complete detailed manifest form to identify and track any spent fuel rod or rod fragment transported within the reactor's premises.

Directs the NRC to identify any spent fuel rod or rod fragment transported outside the premises of the civilian nuclear power reactor through use of manifests used by the Department of Transportation.