The United States monitors the stockpile sites through its "national technical means," a euphemism for spy satellites and other intelligence assets, and was confident they have not been breached, State Department spokeswoman Victoria Nuland said.
The spokeswoman also told reporters Libya no longer has the means to turn the yellowcake into fissile material for bombs.
In late 2003 the United States announced that Libya agreed to give up its weapons of mass destruction programs, a decision that paved the way to a rapprochement between the countries after years of enmity.
The United States long accused Libya of sponsoring terrorism, including the 1988 Lockerbie bombing.
As rebel forces have begun to take control of Libya and this week poured into the capital, Tripoli, concerns have been voiced about the security of any residual nuclear material or chemical weapons components.
"All sensitive elements of Libya's nuclear program, including everything that Libya received from the A.Q. Khan network were removed in early 2004," Nuland said, referring to the accused Pakistani proliferator.
"The last of the highly-enriched uranium, the bomb-making fuel, was removed from Libya in 2009," she added.
The spokeswoman said that Libya's store of yellowcake - a uranium concentrate extracted from ore - was held at Libya's Tajura Nuclear Research facility.
"We believe that it is secure and in any case, Libya doesn't have the means right now to turn yellowcake into anything dangerous, she said.
She said Libyan mustard agent is stored at the Waddan Ammunition Reservation inside massive steel containers within heavy bunkers that have been sealed by an independent international organization.
"Our judgment is that they remain secure," she added.
