"We have identified, disbanded and secured more than 5,000 MANPADS, while thousands more have been destroyed during NATO bombing," Andrew Shapiro, assistant secretary of state for political and military affairs, told reporters.
MANPADS, or man-portable air-defense systems, are guided weapons that are a threat to low-flying aircraft, especially helicopters. They are also capable of being guided to shoot down commercial airliners.
Libyan dictator Moammar Gadhafi had an estimated 20,000 missiles before the uprising that ousted him began in February.
A U.S. State Department official told ABC News the U.S. and Libyan bomb-disposal teams were "still working to assess" how many live stray missiles were unaccounted for.
House Intelligence Committee Chairman Mike Rogers, R-Mich., told USA Today in October an untold number of missiles may have been smuggled out of Libya. He said al-Qaida would like to get its hands on the MANPADS, which can fit in a car trunk.
His remarks followed September comments by European Union Counterterrorism Coordinator Gilles de Kerchove that al-Qaida's North African Organization in the Islamic Maghreb had obtained a stockpile of surface-to-air missiles from Libya.
Most of Libya's stockpiles are Soviet Union-era SA-7 Grail MANPADS, low-altitude surface-to-air missile systems with high-explosive warheads and passive infrared homing guidance, U.S. officials said.
Missiles like those have been used in attacks on 40 aircraft, causing 28 crashes and more than 800 deaths since 1975, USA Today said.
They have also been used, along with other MANPAD systems, by insurgent groups in the Iraq and Afghan wars.
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