The Democratic nominee also accused her rival Donald Trump of making statements that were a "gift to the ISIS".
In the second presidential debate, Clinton used the phrase "violent jihadist terrorists" but insisted that the US is not at war with Islam.
"Right now, a lot of (Muslim majority) nations are hearing what Donald says and wondering why should we cooperate with the Americans (in fighting against IS) and this is a gift to ISIS and the terrorists," she said.
She was responding to a question from a Muslim woman in the audience who asked about Islamophobia and Trump's previous statements about enforcing a ban on Muslims entering the US.
Trump said his policy on Muslim immigration had "morphed" into "extreme vetting". He also said that Clinton cannot fight terrorism as she cannot say the expression "radical Islamic terror".