Safe Climate Act of 2006

Safe Climate Act of 2006 - Amends the Clean Air Act to direct the Environmental Protection Agency (EPA) to promulgate: (1) targets for a 2% reduction in greenhouse gas emissions each year from 2010-2050 ; and (2) regulations requiring reductions to meet such targets, including by setting caps on emissions of sources and sectors with the largest emissions or the best opportunities to reduce them, by issuing and authorizing trading of emission allowances, and by imposing penalties for excess emissions.

Requires relevant federal agencies to finalize a rule to carry out the National Academies' recommendations for regulatory action needed to reduce atmospheric greenhouse gas concentrations or explain their reasons for declining to act.

Requires the President to submit to Congress a plan for the distribution of emission allowances (including through auctions) and the use of proceeds (to be deposited in a Climate Reinvestment Fund) for specified goals, including mitigating the effects of energy cost increases and climate change.

Requires the EPA to ensure that emissions and allowances are accurately tracked, reported, and verified.

Authorizes the emission reduction regulations to include: (1) additional requirements for any source or sector; and (2) performance standards, best management practices, and technology-based requirements. Requires such regulations to set standards for the reduction of greenhouse emissions from motor vehicles at least as quickly as the standards adopted by the California Air Resources Board at its September 2004 hearing. Requires the EPA to revise such standards in 2014 and every five years thereafter to further reduce emissions.

Amends the Public Utility Regulatory Policies Act of 1978 to direct the Secretary of Energy to: (1) require, beginning in 2009, an annual increase in the percentage of electric energy generated from renewable sources that is sold at the retail level in the United States and to require such percentage to be at least 20% of the total electricity sold by 2020; and (2) set end-user savings targets for retail electric-energy and natural gas suppliers. Authorizes DOE to: (1) increase the required percentage of end-user savings for years after 2020; and (2) allow suppliers to achieve the targets through a market-based trading system.