State Department spokeswoman Victoria Nuland later said Kerry misspoke, and that concerns over al-Qaida are related to the rebels.
Speaking to reporters in Washington, she cautiously addressed the effort by opposition members meeting in Istanbul to form an interim government, saying only that the opposition should maintain unity and represent all Syrians with "the best standards of justice, human rights, democracy."
Nuland also confirmed that Syrian warplanes hit targets across the border in Lebanon on Monday in what she described as a "significant escalation."
"These kinds of violations of sovereignty are absolutely unacceptable," she said.
Syria's civil war has pushed millions of people from their homes. The U.N. says more than 70,000 people have been killed.
Associated Press writers Robert Burns and Donna Cassata contributed to this report.
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