Containers are stacked at the port of Bangkok last month. The Obama administration has failed to meet a legal deadline for scanning all shipping containers for radioactive material before they reach U.S. ports. (Dario Pignatelli/Bloomberg News)

The Obama administration has failed to meet a legal deadline for scanning all shipping containers for radioactive material before they reach the United States, a requirement aimed at strengthening maritime security and preventing terrorists from smuggling a nuclear device into any of the nation’s 300 sea and river ports.

The Department of Homeland Security was given until this month to ensure that 100 percent of inbound shipping containers are screened at foreign ports.

But the department’s secretary, Janet Napolitano, informed Congress in May that she was extending a two-year blanket exemption to foreign ports because the screening is proving too costly and cumbersome. She said it would cost $16 billion to implement scanning measures at the nearly 700 ports worldwide that ship to the United States.

Instead, the DHS relies on intelligence-gathering and analysis to identify “high-risk” containers, which are checked before being loaded onto ships. Under this system, fewer than half a percent of the roughly 10 million containers arriving at U.S. ports last year were scanned before departure. The DHS says that those checks turned up narcotics and other contraband but that there have been no public reports of smuggled nuclear material.

In response to the 9/11 Commission, Congress passed a law in 2007 specifying that no cargo container may enter the United States before being scanned with imaging equipment and a radiation-detection device.

The administration’s failure to meet the deadline has left some members of Congress and outside experts concerned about whether the threat is being taken seriously enough.

“I personally do not believe they intend to comply with the law,” Rep. Edward J. Markey (D-Mass.), co-author of the 2007 law, said in an interview. “This is a real terrorist threat, and it has a solution. We can’t afford to wait until a catastrophic attack.”

The DHS says monitors scan 99 percent of the containers for radiation after they arrive at U.S. ports. But experts say the monitors at U.S. ports are not sophisticated enough to detect nuclear devices or highly enriched uranium, which emit low levels of radiation.

The Government Accountability Office has warned that a nuclear device could be detonated while at a port — containers often sit for days awaiting radiation checks — causing billions of dollars in damage in addition to the loss of life. Estimates of damage caused by a nuclear detonation at a major port range from tens of billions of dollars to $1 trillion.

Shipping containers are potentially ideal for smuggling weapons, people and other illicit cargo; ensuring the integrity of the contents is difficult and costly. The standard container is 40 feet long and 8 feet high and holds more than 30 tons of cargo. A large vessel carries 3,000 or more containers from hundreds of different shippers and many ports. And a single container can hold cargo from many customers.

Counterterrorism experts have worried about port vulnerability since the Sept. 11, 2001, attacks. Khalid Sheik Mohammed, the self-described mastermind of the attacks, reportedly told interrogators he had considered sending explosives to the United States hidden inside a shipment of personal computers from Japan.

Graham Allison, a Harvard University political scientist and author of a best-selling book on nuclear terrorism, said that a nuclear device is more likely to arrive in a shipping container than on a missile. But he acknowledged that preventing such an attack is expensive and that there is no guarantee prevention measures will work.

“The game between hiders and seekers is dynamic, and there is no 100 percent solution,” Allison said in an e-mail interview. “The cost-benefit trade-off is the toughest issue.”

Markey and some counterterrorism experts say that the costs of checking every U.S.-bound container could be substantially lower than the DHS estimate and that the necessary measures could be easier to implement than the agency has suggested. Research by scholars at the University of Pennsylvania’s Wharton School indicate that 100 percent of containers could be screened much more inexpensively with existing methods. A number of companies also are developing cheaper new screening technology.

Peter Boogaard, a DHS spokesman, said the department is committed to using a variety of measures, including screening, scanning and working with foreign authorities, to ensure that all goods are secure.

Pilot programs established to scan all containers were abandoned in 2009 after the agency said costs were too high and the effort led to cargo delays and logistical problems.

The current screening system relies heavily on the Customs and Border Protection agency and focuses on a small percentage of goods identified as high-risk through intelligence and analytical software. The program operates at 58 overseas ports that account for 80 percent of the cargo shipped to the United States.

“Our layered and risk-based approach provides that, at a minimum, 100 percent of high risk containers are examined through a number of measures, including screening, scanning, physical inspection, or resolution by foreign authorities,” Napolitano told Congress in her May 2 letter invoking the two-year exemption.

Kevin McAleenan, a senior CBP official, told Congress this year that the program led to inspections of 45,500 suspect containers overseas in 2011 — roughly two containers a day at each of the 58 ports in the program.

Stephen Flynn, a terrorism expert at Northeastern University and a former Coast Guard commander who has studied container security, said, “The current system is woefully inadequate for stopping any determined adversary who wants to get a weapon of mass destruction into the United States.”