Local Port Security Act of 2006 - Authorizes the owner of a U.S. port to file an action seeking relief (including nullification of any contractual obligation with any marine terminal operator) in U.S. district court if a merger, acquisition, or takeover would result in the ownership of a marine terminal operator being controlled by a foreign entity. Requires the Secretary of Homeland Security to: (1) review any such proposed change to determine any potential security concerns; and (2) transmit such review to the marine terminal operator and to the President for purposes of a certain mandatory investigation to determine the effects on national security of such mergers, acquisitions, and takeovers which could result in the ownership of a marine terminal operator within a U.S. port being controlled by a foreign entity.