WASHINGTON—The government of Col. Moammar Gadhafi hasn't destroyed significant stockpiles of mustard gas and other chemical-weapons agents, raising fears in Washington about what could happen to them—and whether they may be used—as Libya slides further into chaos.

Tripoli also maintains control of aging Scud B missiles, U.S. officials said, as well as 1,000 metric tons of uranium yellowcake and vast amounts of conventional weapons that Col. Gadhafi has channeled in the past to militants operating in countries like Sudan and...