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. 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. In addition, the Pakistanis were suspicious that any American-made technology in their warheads could include a secret kill switch," enabling the Americans to turn off their weapons. 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.