Maritime Pollution Prevention Act of 2008 - (Sec. 3) Amends the Act to Prevent Pollution from Ships (Act) to provide for the adoption of Annex VI (Prevention of Air Pollution From Ships Enforcement) of the International Convention for the Prevention of Pollution from Ships, 1973 (MARPOL Convention, which includes any Protocols or Annexes entered into force for the United States). Makes the Act, with respect to Annex VI, applicable to: (1) ships in a port, shipyard, offshore terminal, or U.S. internal waters; (2) a ship that is bound for, or departing from, a port, shipyard, offshore terminal, or the internal waters of the United States and is in navigable U.S. waters or the U.S. Exclusive Economic Zone (EEZ), an emission control, or other specified area; (3) a ship that is entitled to fly the flag of, or operating under the authority of, a party to Annex VI and is in navigable U.S. waters or the EEZ, an emission control, or other specified area; and (4) any other ship to the extent that, and in the same manner as, such ship may be boarded to implement or enforce any other U.S. law or Annex I, II, or V of the Convention, and that is in the EEZ or an emission control or other specified area. Authorizes, but does not require with respect to Annex VI, federal agency heads to determine that some or all Act requirements apply regarding vessel air emissions for public vessels operated under an agency's authority. Prohibits construing provisions relating to ships that are subject to preventive measures to restrict in a manner inconsistent with international law navigational rights and freedoms as defined by U.S. law, treaty, convention, or customary international law.

(Sec. 5) Permits only the Administrator (the Administrator) of the Environmental Protection Agency (EPA), and no other person, to issue Engine International Air Pollution Prevention certificates in accordance with Annex VI and the International Maritime Organization's Technical Code on Control of Emissions of Nitrogen Oxides from Marine Diesel Engines, on behalf of the United States for a documented U.S. vessel.

(Sec. 6) Gives a certificate issued by a country that is a party to the MARPOL Protocol of 1978 (MARPOL Protocol, which includes the Convention) the same validity as a certificate issued by the Secretary of the department in which the Coast Guard (the Secretary) is operating (currently) or the Administrator.

(Sec. 7) Requires the Secretary and the Administrator, after consulting with appropriate federal agencies, jointly to prescribe regulations setting criteria for determining the adequacy of reception facilities for receiving ozone depleting substances, equipment containing such substances, and exhaust gas cleaning residues at a port or terminal, and stating any additional measures and requirements as are appropriate to ensure such adequacy. Permits denial of entry to a ship to a port without adequate reception facilities to receive such substances and residues.

(Sec. 8) Authorizes the Secretary to inspect a ship to which the Act applies to verify whether the ship is in compliance with Annex VI to the Convention and the Act and permits either the Secretary or the Administrator to undertake enforcement actions if an inspection or any other information indicates that there is a violation.

(Sec. 9) Authorizes the Secretary of State, after consulting with the Secretary (currently) or the Administrator, to act for the United States on Protocol and related amendments, including proposed amendments to Annex VI to the Protocol.

(Sec. 10) Permits the Administrator (currently, only the Secretary) to assess civil penalties.

(Sec. 12) Allows any person having an interest which is, or can be, adversely affected to bring an action on his own behalf against the Administrator for a failure to perform any nondiscretionary act or duty.
Output: To amend the Act to Prevent Pollution from Ships to implement MARPOL Annex VI.