WASHINGTON, Nov. 17 — Over 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 American officials say is nowhere near completion, even though it was supposed to be in operation this year.
A raft of equipment — from helicopters to night-vision goggles to nuclear detection equipment — was given to Pakistan to help secure its nuclear material, its warheads, and the laboratories that were the site of the worst known case of nuclear proliferation in the atomic age.
While American officials say that they believe the arsenal is safe at the moment, and that they take at face value Pakistani assurances that security is vastly improved, in many cases the Pakistani government has been reluctant to show American 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 fuel 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,ï¿½? or PALS, a system used to keep a weapon from detonating without proper codes and 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.
In addition, the Pakistanis were suspicious that any American-made technology in their warheads could include a secret “kill switch,ï¿½? enabling the Americans to turn off their weapons.
While many nuclear experts in the federal government favored offering 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, based on interviews with a range of American officials and nuclear experts, some of whom were concerned that Pakistan’s arsenal remained vulnerable. 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.
Since then, some elements of the program have been discussed in the Pakistani news media and in a presentation late last year by the leader of Pakistan’s nuclear safety effort, Lt. Gen. Khalid Kidwai, who acknowledged receiving “internationalï¿½? help as he sought to assure Washington that all of the holes in Pakistan’s nuclear security infrastructure had been sealed.
The Times told the administration last week that it was reopening its examination of the program in light of those disclosures and the current instability in Pakistan. Early this week, the White House withdrew its request that publication be withheld, though it was unwilling to discuss details of the program.
In recent days, American officials have expressed confidence that Pakistan’s nuclear arsenal is well secured. “I don’t see any indication right now that security of those weapons is in jeopardy, but clearly we are very watchful, as we should be,ï¿½? Adm. Mike Mullen, chairman of the Joint Chiefs of Staff, told a Pentagon news conference on Thursday.
Admiral Mullen’s carefully chosen words, a senior administration official said, were based on two separate intelligence assessments issued this month that had been summarized in briefings to Mr. Bush. Both 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 reluctance to provide access 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 — including the laboratory named for Abdul Qadeer Khan, the man who sold Pakistan’s nuclear technology to Iran, North Korea and Libya.
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, like 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,ï¿½? 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,ï¿½? a former official involved in the program said in a recent interview, “and you are never sure what you really accomplished.ï¿½?
So far, the amount the United States has spent on the classified nuclear security program, less than $100 million, amounts to slightly less than one percent of the roughly $10 billion in known American aid to Pakistan since the Sept. 11 attacks. Most of that money has gone for assistance in counterterrorism activities against the Taliban and Al Qaeda.
The debate over sharing nuclear security technology began just before then-Secretary of State Colin L. Powell was sent to Islamabad after the Sept. 11 attacks, as the United States was preparing to invade Afghanistan.
“There were a lot of people who feared that once we headed into Afghanistan, the Taliban would be looking for these weapons,ï¿½? said a senior official who was involved. But a legal analysis found that aiding Pakistan’s nuclear weapons program — even if it was just with protective gear — would violate both international and American law.
General Musharraf, in his memoir, “In the Line of Fire,ï¿½? published last year, did not discuss any equipment, training or technology offered then, but wrote: “We were put under immense pressure by the United States regarding our nuclear and missile arsenal. The Americans’ concerns were based on two grounds. First, at this time they were not very sure of my job security, and they dreaded the possibility that an extremist successor government might get its hands on our strategic nuclear arsenal. Second, they doubted our ability to safeguard our assets.ï¿½?
General Musharraf was more specific in an interview two years ago for a Times documentary, “Nuclear Jihad: Can Terrorists Get the Bomb?ï¿½? Asked about the equipment and training provided by Washington, he said, “Frankly, I really don’t know the details.ï¿½? But he added: “This is an extremely sensitive matter in Pakistan. We don’t allow any foreign intrusion in our facilities. But, at the same time, we guarantee that the custodial arrangements that we brought about and implemented are already the best in the world.ï¿½?
Now that concern about General Musharraf’s ability to remain in power has been rekindled, so has the debate inside and outside the Bush administration about how much the program accomplished, and what it left unaccomplished. A second phase of the program, which would provide more equipment, helicopters and safety devices, is already being discussed in the administration, but its dimensions have not been determined.
Harold M. Agnew, a former director of the Los Alamos weapons laboratory, which designed most of the United States’ nuclear arms, argued that recent federal reluctance to share warhead security technology was making the world more dangerous.
“Lawyers say it’s classified,ï¿½? Dr. Agnew said in an interview. “That’s nonsense. We should share this technology. Anybody who joins the club should be helped to get this.ï¿½?
“Whether it’s India or Pakistan or China or Iran,ï¿½? he added, “the most important thing is that you want to make sure there is no unauthorized use. You want to make sure that the guys who have their hands on the weapons can’t use them without proper authorization.ï¿½?
In the past, officials say, the United States has shared ideas — but not technologies — about how to make the safeguards that lie at the heart of American weapons security. The system hinges on what is essentially a switch in the firing circuit that requires the would-be user to enter a numeric code that starts a timer for the weapon’s arming and detonation.
Most switches disable themselves if the sequence of numbers entered turns out to be incorrect in a fixed number of tries, much like a bank ATM does. In some cases, the disabled link sets off a small explosion in the warhead to render it useless. Delicate design details involve how to bury the link deep inside a weapon to keep terrorists or enemies from disabling the safeguard.
The most famous case of nuclear idea sharing involves France. Starting in the early 1970s, the United States government began a series of highly secretive discussions with French scientists to help them improve the country’s warheads.
A potential impediment to such sharing was the 1968 Nuclear Nonproliferation Treaty, which bars cooperation between nations on weapons technology.
To get around such legal prohibitions, Washington came up with a system of “negative guidance,ï¿½? sometimes called “20 questions,ï¿½? as detailed in a 1989 article in Foreign Policy. The system let United States scientists listen to French descriptions of warhead approaches and give guidance about whether the French were on the right track.
Nuclear experts say sharing also took place after the cold war when the United States worried about the security of Russian nuclear arms and facilities. In that case, both countries declassified warhead information to expedite the transfer of safety and security information, according to federal nuclear scientists.
But in the case of China, which has possessed nuclear weapons since the 1960s and is a signatory to the Nuclear Nonproliferation Treaty, the Clinton administration decided that sharing PALS would be too risky. Experts inside the administration feared the technology would improve the Chinese warheads, and could give the Chinese insights into how American systems worked.
Officials said Washington debated sharing security techniques with Pakistan on at least two occasions — right after it detonated its first nuclear arms in 1998, and after the terrorist attack on the United States in 2001.
The debates pitted atomic scientists who favored technical sharing against federal officials at such places as the State Department who ruled that the transfers were illegal under the Nuclear Nonproliferation Treaty and under United States law.
In the 1998 case, the Clinton administration still hoped it could roll back Pakistan’s nuclear program, forcing it to give up the weapons it had developed. That hope, never seen as very realistic, has been entirely given up by the Bush administration.
The nuclear proliferation conducted by Mr. Khan, the Pakistani metallurgist who built a huge network to spread Pakistani technology, convinced the Pakistanis that they needed better protections.
“Among the places in the world that we have to make sure we have done the maximum we can do, Pakistan is at the top of the list,ï¿½? said John E. McLaughlin, who served as deputy director of the Central Intelligence Agency at the time, and played a crucial role in the intelligence collection that led to Mr. Khan’s downfall.
“I am confident of two things,ï¿½? he added. “That the Pakistanis are very serious about securing this material, but also that someone in Pakistan is very intent on getting their hands on it.ï¿½?