US secrets that may have come from human spies in the field were discovered in the basement at Mar-a-Lago.
The disclosure came as a court released a redacted version of the 32-page FBI affidavit which led to a raid on Donald Trump's Florida home on August 8.
It showed that 14 of the 15 boxes recovered from Mar-a-Lago by the National Archives in January contained classified documents, including some marked "HCS".
In the affidavit, an FBI Special Agent wrote: "HUMINT Control System, or 'HCS', is an SCI [Sensitive Compartmented Information] control system designed to protect intelligence information derived from clandestine human sources, commonly referred to as 'human intelligence'.
"The HCS control system protects human intelligence-derived information, and information relating to human intelligence activities, capabilities, techniques, processes, and procedures."
Steve Hall, former CIA Chief of Russia operations, said: "That's basically information from human spies. 'HCS' stuff, basically, means there's information in those boxes in the basement in Mar-a-Lago that pertain to, or potentially came from, human sources, human spies.
"In the case of human sources, they usually get imprisoned, or if it's Russia or another authoritarian society they're oftentimes simply executed. That type of information is incredibly sensitive."
He added: "As a former CIA guy it sends chills up and down my spine that there's HCS information in somebody's basement. It's really, really bad."
Harry Litman, a former US attorney, said such documents were "radioactive". He told CNN: "The top secret stuff...can get people killed. it is completely alarming."
On the first page of the affidavit seeking a warrant to raid Mar-a-Lago, an FBI Special Agent wrote: "The government is conducting a criminal investigation concerning the improper removal and storage of classified information in unauthorised spaces, as well as the unlawful concealment or removal of government records."
The affidavit showed that the boxes obtained by the National Archives before the raid had contained a total of 184 documents with classification markings.
Of those, 25 were marked "top secret", 92 "secret", and 67 "confidential".
The affidavit said the boxes contained notes written by Mr Trump when he was president.
There were "newspapers, magazines, printed news articles, photos, miscellaneous print-outs, notes, presidential correspondence, personal and post-presidential records, and 'a lot of classified records'.
"Of most significant concern was that highly classified records were unfoldered, intermixed with other records, and otherwise unproperly identified."
The FBI special agent wrote: "Based on my training and experience, I know that documents classified at these levels typically contain NDI [National Defence Information]. Several of the documents also contained what appears to be FPOTUS's [Mr Trump's] handwritten notes."
In addition to "HCS" markings, there were also documents marked "FISA", meaning they were protected by Foreign Intelligence Surveillance Act.
Others were marked "NOFORN" meaning they were not to be released to foreign governments, organisations or citizens.
After reviewing what was in the boxes the FBI "opened a criminal investigation" to determine how "records were removed from the White House" and "whether any additional classified documents or records may have been stored in an unauthorised location".
The Special Agent wrote: "There is probable cause to believe that additional documents that contain classified NDI, or that are presidential records subject to record retention requirements, currently remain at the premises [Mar-a-Lago].
"There is also probable cause to believe that evidence of obstruction will be found at the premises."
The Special Agent added that he had "training at the FBI Academy located at Quantico, Virginia, specific to counterintelligence and espionage investigations."
After the affidavit led to a search warrant, the FBI raided Mr Trump's home and recovered another 11 sets of classified documents.
Mr Trump has accused the FBI and the Biden administration of conducting a politically-motivated witch hunt.
Following the release of the affidavit, Mr Trump noted that it was heavily redacted, and accused the judge who authorised its release of "allowing the break-in of my home".
He added: "Obama must be very proud of him [the judge] right now!"
Asked if he thought national security was threatened by documents found at Mar-a-Lago, President Joe Biden said: "Let the Justice Department determine that. See what happens."
Asked if his predecessor could have declassified the documents, Mr Biden said sarcastically: "I've declassified everything in the world, I'm president. C'mon... declassified everything."
He added: "I'm not going to comment because I don't know the detail. I don't even want to know. I'll let the Justice Department take care of that."
Asked if it was ever appropriate for a president to take home classified and top secret documents, Mr Biden said it "depends on the circumstances".
Mr Biden said he was taking home on Friday the president's daily brief and he had a secure space at home and the military with him.
He said: "I read it, lock it back up, and give it to the military."
When asked if it was appropriate to handle classified documents in an area not specially constructed for this purpose, he said it "depends on the document and depends how secure the venue."
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