The New York-based organization said for months it has been warning Libya's ruling National Transitional Council and NATO about the dangers posed by the weapons and the urgent need to secure them.
"Now that the fighting has ended, one of the NTC's top priorities should be securing weapons facilities, and bringing the unchecked flow of arms in the country under control," said Peter Bouckaert, the group's emergencies director.
Brouckaert added there is no time to waste.
"Surface-to-air missiles can take down civilian aircraft, and the explosive weapons can be converted easily into the car bombs and IEDs that have killed thousands in Iraq and Afghanistan," said Bouckaert.
The United States has sent a team of experts to Libya to help the NTC locate missing surface-to-air missiles.