Ship, Seafarer, and Container Security Act

Ship, Seafarer, and Container Security Act - Requires certain vessels to be equipped with an automatic identification system when operating in U.S. navigable waters. Requires the Secretary of Transportation to initiate a rulemaking to implement such requirement.

Urges the Secretary to negotiate an international agreement (or amendments to such an agreement) that: (1) provides for a uniform, comprehensive, international system of identification for seafarers that will enable the United States and other countries to establish the identity of any seafarer aboard a vessel within the jurisdiction, including the territorial waters, of the United States or such other country; (2) provides greater transparency with respect to the registration and ownership of vessels entering or operating in U.S. territorial waters; and (3) establishes marine container integrity and anti-tampering standards for marine containers. Requires the Secretary to submit draft legislation to specified congressional committees if negotiations do not result in an agreement or the amendment process fails within a specified period after enactment of this Act.

Directs the Commandant of the Coast Guard to establish: (1) a risk-based system for use in evaluating the potential threat to the national security of the United States of vessels entering U.S. territorial waters; and (2) a system of security zones for U.S. ports, territorial waters, and waterways.