Maritime Transportation Security Act of 2004 - (Sec. 2) Amends Federal shipping law to grant U.S. district courts jurisdiction to restrain violations of certain port security requirements. Authorizes the Secretary of Transportation (Secretary) to refuse or revoke port clearance to any owner, agent, master, officer, or person in charge of a vessel that is liable for a penalty or fine for violation of such requirements. Allows any refused or revoked clearance to be granted upon filing of a bond or other surety satisfactory to the Secretary.

Directs the Secretary to require uncleared, unladen imported merchandise remaining on a wharf or pier for more than seven calendar days (not including any time held in Federal custody) to be removed and deposited in a public store or general order warehouse for inspection, after which a delivery permit may be granted. Authorizes the Secretary to impose an administrative penalty of $5,000 on the consignee for each bill of lading for general order merchandise remaining on a wharf or pier in violation of such requirement (except if the violation was a result of force majeure).

(Sec. 3) Shifts from the Secretary to the Administrator of the Maritime Administration responsibility for assessing antiterrorism measures in foreign ports and notifying foreign government authorities of deficiencies and the steps necessary to improve such measures.

Requires the Administrator to identify foreign assistance programs that could facilitate implementation of port security antiterrorism measures in foreign countries. Directs the Administrator and the Secretary to establish a program to utilize those programs that are capable of implementing port security antiterrorism measures at ports in foreign countries that the Secretary finds to lack effective antiterrorism measures.

Directs the Secretary of Homeland Security (DHS Secretary) to report to specified congressional committees on the security of ports in the Caribbean Basin.

(Sec. 4) Amends the Maritime Transportation Security Act of 2002 to direct the Secretary to: (1) establish a curriculum to educate and instruct Federal and State officials on commercial maritime and intermodal transportation; and (2) coordinate with the Federal Law Enforcement Training Center in the curriculum development and the provision of training opportunities for Federal and State law enforcement officials at appropriate law enforcement training facilities.

(Sec. 5) Directs the DHS Secretary to report to specified congressional committees on: (1) recommendations to coordinate background checks for all individuals engaged in transportation activities; and (2) a timeline for implementation of the Transportation Worker Identification Credential in seaports.

(Sec. 6) Directs the DHS Secretary to report to specified congressional committees on the security of ships and facilities used in the cruise line industry, including an assessment of certain security measures employed by the industry.

(Sec. 7) Amends Federal shipping law to direct the Under Secretary of Homeland Security for Border and Transportation Security to establish a maritime transportation security plan grant program to implement Area Maritime Transportation Security Plans and help fund compliance with Federal security plans among port authorities, facility operators, and State and local agencies required to provide security devices.

(Sec. 8) Directs the DHS Secretary to report to specified congressional committees on the design of maritime security grant programs.

Maritime Transportation Security Act of 2004 - Amends Federal shipping law to subject vessels to in rem liability for civil penalties assessed for violation of certain port security requirements and certain reimbursable costs (incurred by a service provider, including port authorities, facility or terminal operators, shipping agents, Federal, State, or local government agencies, or other person to whom management of the vessel at the port is entrusted). Grants U.S. district courts jurisdiction to restrain violations of such requirements. Authorizes the Secretary of Transportation (Secretary) to refuse or revoke port clearance to any owner, agent, master, officer, or person in charge of a vessel that is liable for a penalty or fine for violation of port security requirements.

Directs the Secretary to require uncleared, unladen imported merchandise remaining on a wharf or pier for more than five days to be removed and deposited in a public store or general order warehouse for inspection, after which a delivery permit may be granted.

Directs the Secretary of Homeland Security (HS Secretary) to review U.S. ports and report to Congress on the practices and policies in place to secure shipment of empty containers.

Requires the HS Secretary to submit to Congress: (1) a preliminary plan that provides for the coordination of efforts of Federal agencies in collecting maritime information with respect to vessels, crew, passengers, cargo, and cargo shippers; and (2) a report on an intermodal cargo security plan, including progress in the installation of radiation detectors at all major U.S. seaports, willingness of foreign seaports to utilize non-intrusive inspection methods, and a plan to ensure compliance with security standards that would require ports, terminals, vessel operators, and shippers to adhere to security standards consistent with the National Transportation System Security Plan.

Requires the Department of Homeland Security (DHS) Inspector General to: (1) evaluate the DHS system for targeting international intermodal containers for inspection; and (2) increase the number of containers to be inspected at U.S. ports if such system is ineffective in detecting potential acts of terrorism utilizing such containers.

Directs the Commandant of the U.S. Coast Guard to report to Congress on the potential benefits of establishing joint operational centers for port security at certain U.S. seaports;

Directs the Under Secretary of Homeland Security for Border and Transportation Security to establish a maritime transportation security plan grant program to implement Area Maritime Transportation Security Plans and help fund compliance with Federal security plans among port authorities, facility operators, and State and local agencies required to provide security services.

Requires the Administrator of the Maritime Administration to identify foreign assistance programs that could facilitate implementation of port security antiterrorism measures in foreign countries.

Amends the Maritime Transportation Security Act of 2002 to direct the Secretary to establish a curriculum to educate and instruct Federal and State officials on commercial maritime and intermodal transportation.

Shifts from the Secretary to the HS Secretary the authority to conduct research and development (R&D) on making U.S. ports safer and more secure.

Requires the Secretary to identify nuclear facilities near navigable waterways and evaluate the adequacy of their security plans to protect them from damage by a transportation security incident.

Requires the HS Secretary to: (1) recommend to specified congressional committees ways to coordinate background checks for all individuals engaged in transportation activities; and (2) assess and collect an international port security service fee on commercial maritime transportation entities and an international maritime transshipment security user fee on shippers of cargo and passengers.

Establishes in DHS the Port Security Capital Fund to provide financial assistance to entities required to provide transportation security services.