WASHINGTON — At a busy border crossing, a truck passing through a radiation scanner sets off an alarm. It could be a nuclear device, but it’s far more likely to be kitty litter, ceramic tile, or a load of bananas.

“Nuclear materials such as uranium and plutonium are not the only materials that emit radiation,” Vayl Oxford, who directs the Homeland Security Department’s nuclear office, told a House appropriations panel yesterday.

The machines, first installed after the September 11, 2001, attacks, measure gamma radiation, but they cannot distinguish between low levels of gamma rays that occur naturally in innocent materials, and the makings for weapons that terrorists might use.

So the inspectors must pull the truck or container aside for a second inspection with a hand-held scanner, which, at the nation’s busiest ports or border crossings, can lead to backed-up lines that anger drivers and slow commerce.

“Naturally occurring radioactive materials … place an enormous burden on our customs offices, who must respond to all radiation alarms, including those caused by innocent goods,” Mr. Oxford told the appropriations subcommittee for homeland security. He explained that distance, dense materials like steel and lead, and the speed at which trucks carrying cargo move — about 5 mph — all affect the scanners’ effectiveness.

That’s the dilemma of protecting America from nuclear terrorism — a trade-off among accuracy, inconvenience, and the expense to taxpayers. “The 11 million containers that transit the ports every year [are] an enormous moving haystack that could conceal a deadly needle,” said Rep. Hal Rogers, a Republican of Kentucky.

Government agencies need “to find this proverbial needle in the haystack and prevent it from causing real harm in a way that does not bring the American economic engine to a grinding halt,” Mr. Rogers said.

About 600 scanners have been installed at ports and border crossings around the country. Officials are working with several companies to develop new nuclear detectors that won’t waste time and that can actually differentiate the potassium in a banana from that in highly enriched uranium.

Tests being conducted in Nevada this month pit new detectors against the older ones, to determine whether the higher accuracy claimed by the makers of the new machines is enough to justify their higher cost — around $377,000 each, more than six times the cost of the older models.

Later this spring, the new machines will undergo a real-world test on the New York waterfront so customs officers can judge for themselves if they’re an improvement. They’re also to be used in similar tests along roads leading to the city as part of an effort to set up a protective perimeter starting in 2008.

Some investigators question whether cutting the time wasted by false alarms might actually increase the deadly possibility of nuclear material slipping by an inspector.

Last October, the congressional Government Accountability Office reported that the new machines, touted as having fewer false alarms, showed a frightening incidence of “false negatives” — meaning the scanner either misidentified the material as nonthreatening or failed to detect it at all. That danger is particularly high if the nuclear material is placed beside a nonthreatening substance such as kitty litter, the report said.

Al Qaeda and like-minded terrorists have shown a desire both to obtain nuclear materials and to produce mass casualties.

“Criminals and terrorists can obtain a key component for producing nuclear weapons and smuggle it undetected through the airports of countries on high alert against terrorist threats,” concluded a report published in February by the EastWest Institute, a think tank that studies global security issues.

In a 2006 report, the U.N. International Atomic Energy Agency listed 16 confirmed incidents of trafficking in highly enriched uranium or plutonium globally from 1993 to 2005.

Concerns about terrorists obtaining nuclear material increased dramatically after the attacks of September 11, 2001, but the Bush administration’s efforts to deal with the issue were scattered across different agencies.

As early as 2002, the GAO lamented the lack of any government-wide plan to guide America’s efforts to combat nuclear smuggling. It said “some programs were duplicative, and coordination among U.S. agencies was not effective.”

It was not until April 2005 that the Domestic Nuclear Detection Office, which Mr. Oxford heads, was created in the Homeland Security Department to coordinate the government’s development of technology to detect nuclear materials.