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More than a year after Congress told the Energy Department to harden the nation’s nuclear bomb factories and laboratories against terrorist raids, five of the 11 sites are certain to miss their deadlines, some by many years, the Government Accountability Office has found.

The Energy Department has put off security improvements at some sites that store plutonium because it plans to consolidate the material at central locations, but the GAO said in a Senate briefing that the project is also likely to lag. A copy of the briefing materials was provided to The New York Times by a private group, the Project on Government Oversight, which has long been pushing for better security at the weapons sites.

Danielle Brian, the group’s executive director, said that although the deadline set by Congress was tight, if the Energy Department “had taken seriously consolidating and making this an expedited effort, they wouldn’t be having these problems now.”

Robert Alvarez, an adviser to the energy secretary in the Clinton administration, said there was wide agreement that centralizing the fuel was a good idea. But Alvarez added, “There’s a lot of pushback about moving fissile materials from a site, because then you lose a portion of your budget and prestige.”

The Energy Department declined requests for an interview, but Michael Kilpatrick, a deputy chief at the department’s Office of Health, Safety and Security, said in a statement that the steps under way were “further enhancements and better protection to some of the most secure facilities in the country.”

One site that will miss its deadline by years is the Oak Ridge National Laboratory in Tennessee, which holds a large stock of weapons-usable uranium. The laboratory plans to dilute the uranium, but that will take until 2015, the auditors found.

Two other sites that will miss their deadlines are operated by the National Nuclear Security Administration, which is responsible for weapons security. The agency was established in 1999 after a number of security breaches in the weapons complex, and in January its director was forced to resign because of other security lapses.

After the 9/11 attacks, the Energy Department changed its “design basis threat,” the description of the attacking force against which the weapons sites should prepare their defenses. The details of this hypothetical design basis threat are classified, but the new definition specifies a larger and more capable group of attackers.

To emphasize the importance of the preparations, Congress wrote into law that the Energy Department sites should submit plans on how it would meet the requirements. Recognizing that much of the department’s work runs far behind schedule, Congress specified that if a delay were necessary, it would have to be approved by the secretary or deputy secretary of energy.

The Energy Department told Congress in 2006 that six sites would meet the 2008 deadline. But the accountability office said one of those, the Oak Ridge National Laboratory, would not make the deadline.