"We knew they were up to no good," said Henry Sokolski, the Pentagon's top arms control official in 1990.
The Pakistani scientist at the center of the nuclear network, Abdul Qadeer Khan, made a public confession this month and said Pakistan's leadership was unaware and uninvolved. President Pervez Musharraf pardoned Khan a day later.
President Bush has said the United States became aware of Khan's network only in the past few years through daring work by U.S. and British intelligence agents.
"We unraveled the Khan network and we are putting an end to its criminal enterprise," Bush's national security adviser, Condoleezza Rice, said in a speech Thursday.
But Sokolski and Rowen said former President Bush's administration did little to follow up on Beg's warning. "In hindsight, maybe before or after that they did make some transfers," Rowen said.
Ashton Carter, an assistant defense secretary from 1993 to 1996, said he doesn't remember even being told about the problem when he joined the Pentagon.
Rowen said he told Beg that Pakistan would be "in deep trouble" if it gave nuclear weapons to Iran. Rowen said he was surprised by the threat because at the time Americans thought Pakistan's secular government dominated by Sunni Muslims wouldn't aid Iran's Shiite Muslim theocracy.
"There was no particular reason to think it was a bluff, but on the other hand, we didn't know," Rowen said.
Declassified documents and former officials say U.S. officials knew since at least 1983 about Pakistan's extensive underground supply network for its nuclear weapons program, which first tested nuclear explosives in 1998. Former officials say Washington had other murky clues about Pakistani help to Iran and strong suspicions of the North Korea link by the late 1990s.
Most of the middlemen for Khan's network in the 1990s were either investigated or convicted in Europe for supplying Pakistan's nuclear program in the 1980s.