reported.
He was looking into whether Trump kept hundreds of classified documents at his Mar-a-Lago property in Palm Beach, about 70 miles north of Miami.
The former president has also been accused of obstructing the government's effort to recover the classified materials.
Trump allegedly took about 300 documents after vacating the White House. Around 100 were recovered during a raid in August.
The Justice Department declined to comment on the new indictment.
It is the latest hurdle in Trump's attempts to win the Republican nomination and the White House in 2024.
'A DARK DAY' His challengers include former Vice President Mike Pence and Florida Governor Ron DeSantis .
Trump's campaign said on Thursday: “This is un-American and wrong.
"President Trump violated no laws and is being held to a different legal standard than other former Presidents and Vice Presidents.
"We are confident that no matter how crooked the Executive branch has become, the American justice system is resilient and will throw this case out in its entirety. If not, our cherished Constitution is in serious trouble.
“President Trump will fight this unconstitutional abuse of power until he is ultimately vindicated. He will never stop fighting for the American people, and he will continue to work to restore the greatness of the United States of America.”
Kevin McCarthy, Speaker of the House of Representatives, branded the news a "dark day" for the US.
He tweeted: "It is unconscionable for a President to indict the leading candidate opposing him. Joe Biden kept classified documents for decades. I, and every American who believes in the rule of law, stand with President Trump against this grave injustice.
"House Republicans will hold this brazen weaponization of power accountable."
DeSantis, who is behind Trump in the polls to be the Republican nominee for president, has also spoken out.
He said: "The weaponization of federal law enforcement represents a mortal threat to a free society.
"We have for years witnessed an uneven application of the law depending upon political affiliation.
"Why so zealous in pursuing Trump yet so passive about Hillary or Hunter?
"The DeSantis administration will bring accountability to the DOJ, excise political bias, and end weaponization once and for all."
Trump's attorney, Alina Habba, added in an interview with Fox News' Jesse Watters on Thursday: "When your name is Donald Trump, when you're leading in the polls, you are going to get hit hard.
"You are going to get indicted until you can't take it anymore. But they picked the wrong guy.
"And I think that's why he's so ahead in the polls. And that's why he will probably win."
Special counsel Jack Smith has been in charge of the prosecution's case against the former president Credit: AP