"If she gets to pick her judges, nothing you can do folks," Trump told a crowd in Wilmington, North Carolina on Tuesdsay. "Although the Second Amendment people, maybe there is I don't know."
The Trump campaign disputed the interpretation that Trump suggested violence, saying he wanted to unify voters who support the 2nd Amendment.
"It's called the power of unification — 2nd Amendment people have amazing spirit and are tremendously unified, which gives them great political power. And this year, they will be voting in record numbers, and it won't be for Hillary Clinton, it will be for Donald Trump," senior communications advisor Jason Miller said in a statement.
Trump's running mate, Indiana Gov. Mike Pence, brushed off the interpretations of suggested violence. When asked in an interview with the NBC affiliate in Philadelphia whether Trump implied that violence should be used against Clinton, Pence said: "Of course not."
Trump subsequently told Fox News Channel's "Hannity" program that "nobody in that room" thought he meant anything other than to rally support against Clinton, Reuters reported.
"This is a strong powerful movement, the Second Amendment," Trump said, according to Reuters. "Hillary wants to take your guns away. She wants to leave you unprotected in your home. This is a tremendous political movement."
"It sounds just like a joke gone bad," Ryan said. "I hope he clears it up very quickly."
Clinton campaign manager Robby Mook condemned Trump's comments.
"This is simple — what Trump is saying is dangerous. A person seeking to be the President of the United States should not suggest violence in any way," Mook said in a statement.
Threats against Clinton are covered by a special section of the U.S. criminal law code given her status as the wife of a former president and a major party presidential nominee.
Secret Service communications director Cathy Milhoan told NBC News that the "Secret Service is aware of the comments."
Martin Luther King Jr.'s daughter Bernice King wrote in a tweet that she found Trump's comments "distasteful, disturbing, dangerous."
Some politicians took to Twitter to express alarm.
Sen. Chris Murphy, D-Conn., said the comment should not be considered a misstep, instead representing a violent threat "upping the possibility of a national tragedy."
Rep. Brendan Boyle, D-Pa., tweeted that the assassination of a president was "Not in any way a joking matter."
Sen. Elizabeth Warren tweeted that Trump's behavior is a reflection of his underperformance in recent polls.
The National Rifle Association, which has endorsed Trump and is airing ads on his behalf, said his remarks were a call for voters to defend the Second Amendment and vote against Clinton.
-Reuters and Associated Press contributed to this article