Some government agencies, Mr. Miller said, did anticipate a crisis, but the Homeland Security Department appears not to have gotten the message.

The department had planned a worldwide network using the new detectors, which were supposed to detect plutonium or uranium in shipping containers. The government wanted 1,300 to 1,400 machines, which cost $800,000 each, for use in ports around the world to thwart terrorists who might try to deliver a nuclear bomb to a big city by stashing it in one of the millions of containers that enter the United States every year.

At the White House, Steve Fetter, an assistant director of the Office of Science and Technology Policy, said the helium 3 problem was short-term because other technologies would be developed. But, he said, while the government had a large surplus of helium 3 at the end of the cold war, “people should have been aware that this was a one-time windfall and was not sustainable.”

Helium 3 is not hazardous or even chemically reactive, and it is not the only material that can be used for neutron detection. The Homeland Security Department has older equipment that can look for radioactivity, but it does not differentiate well between bomb fuel and innocuous materials that naturally emit radiation  like cat litter, ceramic tiles and bananas  and sounds false alarms more often.

Earlier this year, the Pacific Northwest National Laboratory, part of the Energy Department, said in a report, “No other currently available detection technology offers the stability, sensitivity and gamma/neutron discrimination” of detectors using helium 3.