WASHINGTON -- During the past six years, the Bush administration has spent almost $100 million on a highly classified program to help Gen. Pervez Musharraf, Pakistan's president, secure his country's nuclear weapons, according to current and former senior administration officials.
But with the future of that country's leadership in doubt, debate is intensifying about whether Washington has done enough to help protect the warheads and laboratories, and whether Pakistan's reluctance to reveal critical details about its arsenal has undercut the effectiveness of the continuing security effort.
The aid, buried in secret portions of the federal budget, paid for the training of Pakistani personnel in the United States and the construction of a nuclear security training center in Pakistan, a facility that U.S. officials say is nowhere near completion, even though it was supposed to be in operation this year.
A raft of equipment was given to Pakistan to help secure its nuclear material, its warheads and the laboratories that were the sites of the worst known case of nuclear proliferation in the atomic age.
While U.S. officials say that they believe the arsenal is safe at the moment, and that they take at face value Pakistan's assurances that security is vastly improved, in many cases the Pakistani government has been reluctant to show U.S. officials how or where the gear is actually used.
That is because the Pakistanis do not want to reveal the locations of their weapons or the amount or type of new bomb-grade material that the country is now producing.
The American program was created after the Sept. 11, 2001, attacks, when the Bush administration debated whether to share with Pakistan one of the crown jewels of American nuclear protection technology, known as "permissive action links," or PALS, a system used to keep a weapon from detonating without proper authorizations.
In the end, despite past federal aid to France and Russia on delicate points of nuclear security, the administration decided that it could not share the system with the Pakistanis because of legal restrictions.
While many nuclear experts in the federal government favored offering aid and the PALS system because they considered Pakistan's arsenal among the world's most vulnerable to terrorist groups, some administration officials feared that sharing the technology would teach Pakistan too much about American weaponry. The same concern kept the Clinton administration from sharing the technology with China in the early 1990s.
The New York Times has known details of the secret program for more than three years, but the newspaper agreed to delay publication of the article after considering a request from the Bush administration, which argued that premature disclosure could hurt the effort to secure the weapons.
Early last week, the White House withdrew its request that publication be withheld, though it was unwilling to discuss details of the program.
The secret program was designed by the Energy Department and the State Department, and it drew heavily from the effort over the past decade to secure nuclear weapons, stockpiles and materials in Russia and other former Soviet states. Much of the money for Pakistan was spent on physical security, such as fencing and surveillance systems, and equipment for tracking nuclear material, if it left secure areas.
But while Pakistan is formally considered a "major non-NATO ally," the program has been hindered by a deep suspicion among Pakistan's military that the secret goal of the United States was to gather intelligence about how to locate and, if necessary, disable Pakistan's arsenal, which is the pride of the country.
"Everything has taken far longer than it should," a former official involved in the program said in a recent interview, "and you are never sure what you really accomplished."
Two intelligence assessments issued this month that had been summarized in briefings to Bush concluded that Pakistan's nuclear arsenal was safe under current conditions, and one also looked at laboratories and came to the same conclusion.
Still, the Pakistani government's reticence to release information has limited efforts to assess the situation. In particular, some American experts say they have less ability to look into the nuclear laboratories where highly enriched uranium is produced.