National Greenhouse Gas Emissions Inventory Act of 2005

National Greenhouse Gas Emissions Inventory Act of 2005 - Amends the Clean Air Act to require the Administrator of the Environmental Protection Agency (EPA) to establish and administer: (1) a national greenhouse gas (GHG) emissions information system to collect annual lists required to be submitted under this Act of an entity's GHG emissions; and (2) a national GHG registry (included in such system) to collect voluntarily reported information on emissions reductions.

Directs the Administrator to submit a draft design of the system to Congress and to publish all information in the system through the EPA's website unless national security concerns are present.

Establishes mandatory reporting of GHG emissions for entities that meet specified threshold requirements. Sets forth factors for the adjustment of emissions records by a reporting entity.

Requires the Administrator and the Secretaries of Commerce, Agriculture, and Energy jointly to work with the States, the private sector, and nongovernmental organizations to develop: (1) protocols for quantification and verification of GHG emissions; (2) electronic methods for quantification and reporting of such emissions; and (3) GHG accounting and reporting standards. Requires such protocols and methods to conform to best practices to the extent practicable.

Directs the Administrator to publish, annually, a national GHG emissions inventory and to include in the inventory's analysis a comparison of the indirect emissions of manufactured products reported and the indirect emissions of comparable products carrying the Energy Star label.