Intermodal Shipping Container Security Act

Intermodal Shipping Container Security Act - Directs the Under Secretary of Homeland Security for Border and Transportation Security to take into account a certain National Maritime Transportation Security Plan to ensure that the strategy for dealing with threats to transportation security incorporates relevant aspects of the Plan and addresses all modes of commercial transportation to, from, and within the United States.

Directs the Secretary of Homeland Security to submit to Congress a strategic plan for integrating security for all modes of transportation by which intermodal shipping containers arrive, depart, or move in interstate commerce. Establishes the Senior Steering Group to develop solutions to conflicts among constituent agencies regarding intermodal shipping container security.

Amends Federal shipping law to direct the Secretary of Transportation to develop a system to increase the number of intermodal shipping containers physically inspected (including nonintrusive inspection by scanning technology), monitored, and tracked within the United States. Requires, beginning in 2007, no less than 50 percent of all ocean-borne shipping containers entering the United States to incorporate "Smart Box" or equivalent technology.

Requires the Secretary of Homeland Security to: (1) report to Congress a preliminary plan for strengthening the Bureau of Customs and Border Protection's container targeting system; (2) issue regulations reducing from 60 days to 45 days after arrival at a U.S. port the time period for revisions to a container manifest that is submitted to the Bureau of Customs and Border Protection; (3) develop a system to share threat and vulnerability information with all of the industries in the supply chain; and (4) substantially increase under the Container Security Initiative the number of U.S. Customs Service inspectors assigned to duty outside of the United States with responsibility for inspecting intermodal shipping containers being shipped to the United States.

Directs the Under Secretary to implement a plan for random inspection of shipping containers in addition to any targeted or preshipment inspection of such containers required by law. Sets forth civil penalties for discrepancies found in container manifests.