An Energy Department investigation into a plutonium mix-up reveals deficiencies that the New Mexico nuclear weapons lab must address, an official says.

An Energy Department investigation has alleviated fears that a significant amount of plutonium was missing from a national laboratory, but it has also heightened concerns about flaws in the system for controlling the U.S. stockpile of weapons materials.

The investigation began in February, shortly after a routine inventory at Los Alamos National Laboratory in New Mexico found a plutonium shortage estimated at 2.2 pounds, setting off a frantic national effort to determine what happened to the material.

The confidential investigation concluded this week that statisticians at the lab had miscalculated the amount of plutonium at its facility and that none was actually missing.

Although the finding eliminates the worst-case scenario -- that the material left the facility and ended up in rogue hands -- it raises doubts about the lab's management at a time of growing concern about nuclear terrorism.

Brad Peterson, the Energy Department's chief for defense nuclear security, acknowledged in an interview that the closure of the investigation does not clear the laboratory but rather points out deficiencies that must be addressed.

"There are many corrective actions that need to be taken, and we are watching closely," Peterson said. "We are very concerned, obviously."

The inventory miscalculation follows more than a decade of security problems at the bomb design center, including several incidents of lost classified information contained on computers, electronic drives and paper.

The current case seems to parallel an incident in 2004, when the lab thought it had lost computer disks containing bomb design information.

Operations were shut down for six months while officials conducted an intensive search. In the end, an investigation concluded the disks never existed. Not long after, the laboratory director was fired.

"When you are in the nuclear weapons business, you have to keep precise track of every single thing from classified information to nuclear materials," said Philip Coyle, a veteran nuclear weapons expert who served in both the Energy and Defense departments. "You wonder if Los Alamos doesn't have good statisticians and good inventory systems, who would?"

Energy officials, however, defended their system of safeguards, saying their quick investigation demonstrated to other countries the U.S. commitment to tight controls on nuclear materials.

The incident was brought to public attention by the Project on Government Oversight, a Washington-based watchdog group that has long urged improved nuclear weapons security. The group intercepted a scathing letter sent in February by Energy officials to lab director Michael R. Anastasio, saying that the lab had ignored its deficiencies for a long time.

Peter Stockton, an investigator for the watchdog group and a former security expert at the Energy Department, said Los Alamos is overly confident about protecting plutonium.

"The lab has plenty of holes in its highly touted security system," Stockton said.

Such problems are hardly new. In September 2007, Energy Department Inspector General Gregory H. Friedman detailed problems with Los Alamos' inventory system. In some areas, no inventory had been taken for 10 years, he reported.

Dating back to the Cold War, the lab has checked only a small fraction of its uranium and plutonium stockpile and then statistically computed any imbalances.

Coyle, among others, says the current system should be dumped in favor of an actual inventory of every ounce of nuclear material, known as a "wall-to-wall" inventory.

Peterson said the department is moving in that direction. In the future, the Los Alamos lab will have to conduct a 100% inventory every two months of all materials actively being used in fabrication or research.

But such comprehensive checks will not be done in the lab's plutonium and uranium storage vaults because it could expose workers to more than allowable levels of radiation. The vaults are considered the most secure parts of the facility.

Kevin Roark, a lab spokesman, said there was never any possibility that plutonium was stolen, owing to tight physical security measures that he could not discuss.

Meanwhile, the Energy Department's office in New Mexico has suspended an employee, David Lee, on suspicion that he leaked the February letter.

"They are trying to lay the rap on me," Lee said in an interview, though he would neither confirm nor deny the allegation.

Officials at the local Energy office declined to comment.

Tom Devine, an attorney for the Government Accountability Project, which represents whistle-blowers, said that even if Lee had leaked the unclassified letter, the action was protected under U.S. law.

Source: Ralph Vartabedian of the Los Angeles Times