If found guilty, Bolton could face up to 10 years in prison for each charge. He is expected to surrender to authorities on Friday.
“No one is above the law,” US Attorney General Pam Bondi said in a statement announcing the charges.
Bolton said in a statement that he looked forward to defending his “lawful conduct” in court as he accused Trump of seeking “retribution against me”.
“Now, I have become the latest target in weaponizing the Justice Department to charge those he [Trump] deems to be his enemies with charges that were declined before or distort the facts,” Bolton said.
Bolton’s lawyer, Abbe Lowell, said the charges stemmed from diary entries kept by his client over his 45-year career in public service.
“Like many public officials throughout history, Amb Bolton kept diaries – that is not a crime,” said Mr Lowell.
He described the records as “unclassified, shared only with his immediate family, and known to the FBI as far back as 2021”.
According to CNN, Bolton is alleged to have shared the information with his wife and daughter.
The unauthorised information includes “diary-like entries from Bolton’s time as the National Security Advisor” and were allegedly “printed and stored” at Bolton’s home in Bethesda, Maryland.
Bolton was fired from Trump’s first administration in 2019. His 2020 memoir, The Room Where It Happened, recounted his time working under Trump and portrayed him as a president who was ill-informed about geopolitics.
The White House filed a lawsuit to block the book from being published, arguing it contained classified information and had not been properly vetted. A judge denied the request and the book was released days later.