Of the 38 pages in the unsealed affidavit, 21 are blacked out
Investigators said top secret files had been stored at Mar-a-Lago along with assorted newspapers and magazines.
The justice department said it censored the affidavit to protect "a significant number of civilian witnesses".
Mr Trump said the inquiry was being led by "political Hacks and Thugs".
On Friday, the US Department of Justice released a version of the affidavit used to justify the FBI's incursion into Mr Trump's Mar-a-Lago estate on 8 August, but it has been heavily redacted.
Given that the court papers were filed before the search of the Palm Beach estate, they contain no new details on the 11 sets of classified documents that the justice department has said were recovered from the exclusive golf club.
The FBI agent who drafted the affidavit wrote they had "probable cause" to believe that "evidence, contraband, fruits of crimes or other items illegally possessed" would be discovered.
"There is also probable cause to believe that evidence of obstruction will be found at the premises," the agent added.
The document shows that the unprecedented criminal investigation into a former president began after the National Archives, which maintains historic White House records, identified "a lot" of classified files among 15 boxes that it had recovered from Mar-a-Lago in January this year.
An FBI review of those materials uncovered 184 classified documents, including 25 marked as "Top Secret".
The cache included information from highly sensitive US intelligence human sources. Some items were also marked "Noforn" - meaning they must not be released to foreign nationals.
The files - some of which appeared to show Mr Trump's handwritten notes - were interspersed with newspapers, magazines and other documents, according to the affidavit.
"Of most significant concern was that highly classified records were unfoldered, intermixed with other records and otherwise unproperly identified," the document said.
The discovery led investigators to believe that Mr Trump may have been in violation of three separate federal laws, including the Espionage Act that governs classified information.
Of the 38 pages in the unsealed affidavit, 21 are mostly or entirely blacked out. There are several pages in which not a single word is visible.
Mr Trump acquired Mar-a-Lago in 1985
A separate document explaining the proposed redactions noted that some parts of the affidavit must remain under seal to "protect the safety and privacy of civilian witnesses, in addition to law enforcement personnel, as well as to protect the integrity of the ongoing investigation".
Revealing the identities of witnesses, the document added, could potentially lead to them being subjected to harms including "retaliation, intimidation, or harassment and even threats to their physical safety".
Mr Trump - who may launch another White House campaign for 2024 - reacted angrily on his social media platform, Truth Social.
He said that Judge Bruce Reinhart, who signed off on the search, should never have allowed the "break-in of my home". Mr Trump also accused the judge of "animosity" towards him.
He has maintained that he had already ordered all the documents to be declassified.
The justice department's investigation is now expected to continue behind closed doors as it continues to review the documents and - potentially - call in more witnesses.
The public may not hear from prosecutors about the investigation until a decision has been made on whether it will result in any criminal charges.
-- Courtesy of BBC News