Mr Trump said in a statement that Mar-a-Lago in Palm Beach was "occupied by a large group of FBI agents". The search was reportedly connected to an investigation into Mr Trump's handling of official papers.
US media reports that the search is related to documents the president may have taken to Mar-a-Lago on leaving the White House.
Mr Trump's lawyer, Christina Bobb, told NBC News that some papers had been seized during the search. The dramatic escalation of law enforcement scrutiny of Mr Trump comes as he prepares for a possible third presidential run in 2024.
"These are dark times for our Nation," Mr Trump's statement began. He said he had co-operated with all relevant government agencies, so the "unannounced raid on my home was not necessary or appropriate".
Mr Trump said it amounted to "prosecutorial misconduct" and "the weaponisation of the Justice System" to prevent him from running for the White House again.
"Such an assault could only occur in broken, Third-World Countries," he said. "Sadly, America has become one of those countries, corrupt at a level never seen before.
"They even broke into my safe!" According to CBS News, the BBC's US partner, Mr Trump, was in Trump Tower in New York City during Monday's reported raid.
Eric Trump, the president's second-oldest son, told Fox News that the FBI's execution of the search warrant on Mr Trump's Mar-a-Lago estate was related to an investigation into the handling of National Archives records.
In February, the National Archives, the US government agency that manages the preservation of presidential records, asked the justice department to investigate Mr Trump for his handling of official papers.
The National Archives said it had retrieved 15 boxes from Mar-a-Lago, some of which contained classified records. US presidents must transfer their letters, work documents and emails to the National Archives.
But officials say the former president illegally ripped up many documents. Some of them had to be taped back together, the Archives said. Mr Trump, at the time, rejected reports that he had mishandled official records as "fake news".
A senior Trump adviser in Palm Beach told CBS that the search by federal agents on Mar-a-Lago was about the presidential records. "This is about the PRA [Presidential Records Act]," said the Trump source, who only agreed to speak on condition of anonymity.
"When have you ever heard about a raid because of PRA?" The source added: "They [the FBI] just left, and they left with very little."
A judge must sign a federal search warrant. Law enforcement agencies must have evidence the search is likely to find evidence of illegality.
An unnamed law enforcement official told CBS that the Secret Service was notified shortly before the warrant was served around 10:00 (14:00 GMT) and that agents protecting Mr Trump helped the FBI investigators.
The source said several boxes were removed, adding that no doors were kicked down and that the raid had concluded by the late afternoon.
In a forthcoming book, Confidence Man, New York Times journalist Maggie Haberman will report that staff at the White House residency sometimes found wads of paper clogging a toilet, believing Mr Trump was the flusher.
Ms Haberman has obtained photos showing paper in a toilet bowl at the White House. A senior White House official has told CBS the West Wing was unaware of the FBI raid on Mr Trump's home.
"No advance knowledge," said the senior official, who was not authorised to speak publicly about the matter. "Some learned from old media, some from social media."
US President Joe Biden's White House has said it limits its interactions with top justice department officials to avoid any hint of political pressure or impropriety.
Mr Biden pledged during his White House campaign to stay out of justice department affairs. The president and his family are also waiting to see whether federal prosecutors will indict his son, Hunter Biden, on tax evasion or other federal charges.
In addition to the National Archives inquiry, a US House of Representatives select committee is investigating Mr Trump's actions surrounding the US Capitol riot on 6 January 2021 - when a horde of his supporters rioted at Congress as lawmakers met to certify Mr Biden's election victory.
The US justice department is examining Mr Trump's challenge to the results of the 2020 presidential election. Attorney General Merrick Garland has said he intends to hold "everyone" accountable.
And a prosecutor in Fulton County, Georgia, is also investigating whether Mr Trump and his associates tried to interfere in the state's results from the 2020 election. - BBC