Clinton said that while the actions of President Bashar Assad's government have been deplorable, chemical weapons would bring them to a new level.
"We once again issue a very strong warning to the Assad regime that their behavior is reprehensible, their actions against their own people have been tragic," she said. "But there is no doubt that there's a line between even the horrors that they've already inflicted on the Syrian people and moving to what would be an internationally condemned step of utilizing their chemical weapons."
Activity has been detected before at Syrian weapons sites, believed to number several dozen.
Defense Secretary Leon Panetta said in late September the intelligence suggested the Syrian government had moved some of its chemical weapons in order to protect them. He said the U.S. believed that the main sites remained secure.
Asked Monday if they were still considered secure, Pentagon press secretary George Little declined to comment about any intelligence related to the weapons.
Senior lawmakers were notified last week that U.S. intelligence agencies had detected activity related to Syria's chemical and biological weapons, said a U.S. intelligence official, speaking on condition of anonymity to discuss the closed-door meetings. All congressional committees with an interest in Syria, from the intelligence to the armed services committees, are now being kept informed.
"I can't comment on these reports but I have been very concerned for some time now about Syria's stockpiles of chemical weapons and its stocks of advanced conventional weapons like shoulder-launched anti-aircraft missiles," said House intelligence committee Chairman Mike Rogers, R-Mich. "We are not doing enough to prepare for the collapse of the Assad regime, and the dangerous vacuum it will create. Use of chemical weapons by the Assad regime would be an extremely serious escalation that would demand decisive action from the rest of the world," he added.
Syria is believed to have one of the world's largest chemical weapons programs, and the Assad regime has said it might use the weapons against external threats, though not against Syrians. The U.S. and Jordan share the same concern about Syria's chemical and biological weapons — that they could fall into the wrong hands should the regime in Syria collapse and lose control of them.
Klapper reported from Prague. Associated Press writers Josef Federman in Jerusalem, Albert Aji in Damascus and Matthew Lee, Kimberly Dozier, and Julie Pace in Washington contributed to this report.
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