MARPOL Annex VI Implementation Act of 2006 - (Sec. 4) Applies (with regard to Annex VI of the International Convention for the Prevention of Pollution from Ships, 1973) federal law relating to the prevention of pollution from ships to certain foreign ships. Allows the head of a federal department or agency to apply those provisions of federal law to one or more classes of public vessels operated under the authority of that department or agency.
(Sec. 6) Limits to the Administrator of the Environmental Protection Agency (EPA), on behalf of the United States, issuance of an Engine International Air Pollution Prevention Certificate in accordance with Annex VI to the Convention and the International Maritime Organization's Technical Code on Control of Emissions of Nitrogen Oxides from Marine Diesel Engines. Gives a certificate issued by a country that is a party to the MARPOL Protocol (the Protocol of 1978 relating to and including the Convention) the same validity as a certificate issued by the Secretary (Secretary) of the department in which the Coast Guard is operating or by the Administrator.
(Sec. 7) Requires ports and terminals to ensure the availability of reception facilities for receiving ozone depleting substances, equipment containing such substances, and exhaust gas cleaning residues.
(Sec. 8) Authorizes the Secretary to inspect ships to verify compliance and to take enforcement actions for violations.
(Sec. 9) Authorizes the Secretary of State, after consulting with the Secretary, to act for the United States on Annex VI amendments.