He said that Mrs Clinton would put liberal justices on the Supreme Court if she wins, threatening gun ownership protected by the Second Amendment.
Speaking at a rally in North Carolina, Mr Trump hinted that gun rights advocates could stop her taking power.
That sparked an online backlash, many accusing him of inciting violence.
But his campaign team said he was actually talking about getting gun rights supporters to the ballot box to enact change politically.
The remarks that sparked the firestorm were made at a rally in Wilmington on Tuesday afternoon.
The Republican presidential nominee said: “Hillary wants to abolish, essentially abolish the Second Amendment. By the way, and if she gets to pick her judges, nothing you can do, folks.
“But the Second Amendment people, maybe there is, I don’t know.”
The Second Amendment enshrines the right to bear arms in the US Constitution.
Robby Mook, Mrs Clinton’s campaign manager, said “what Trump is saying is dangerous”.
But Mr Trump’s campaign was quick to respond, saying the candidate was referring to the power of gun rights advocates to vote in large numbers.
“It’s called the power of unification – 2nd Amendment people have amazing spirit and are tremendously unified, which gives them great political power,” the statement read.
“And this year, they will be voting in record numbers, and it won’t be for Hillary Clinton, it will be for Donald Trump.”
The National Rifle Association backed Mr Trump and warned Mrs Clinton would pick judges that would not uphold the Second Amendment.