The New York Times is reporting that over the past six years, the Bush administration has spent almost $100 million on a highly classified program to help Pakistan President Pervez Musharraf secure his country’s nuclear weapons.

Click here to read full New York Times report.

The Times quotes current and former senior administration officials as saying the U.S. is paying for an array of equipment — from helicopters to night-vision goggles to nuclear detection equipment — to help protect Pakistan's nuclear material, its warheads, and laboratories.

The funding, buried in the federal budget, also paid for the training of Pakistani personnel in the U.S. and the construction of a nuclear security training center in Pakistan, it is being reported.

Gordon Johndroe, spokesman for the U.S. National Security Council told FOX Sunday he is confident that Pakistan’s nuclear arsenal is well secured, despite that government’s reluctance to provide U.S. access to some of its facilities.

"At this time, we believe that Pakistan's nuclear weapons and facilities are under the appropriate control of Pakistani authorities."

Meanwhile, another senior official tells FOX that the U.S. has been helping Pakistan to make its nuclear facilities safe and believes the help has paid off.