Originally Published: 26 AUG 22 12:27 ET

Updated: 26 AUG 22 14:15 ET

By Marshall Cohen, Tierney Sneed and Jeremy Herb, CNN

(CNN) -- The FBI told a judge that there was "probable cause to believe" that classified national security materials were improperly taken to "unauthorized" locations at Donald Trump's Mar-a-Lago resort, and that a search would also likely find "evidence of obstruction," according to a redacted version of the search warrant affidavit released Friday.

The affidavit was one of the documents the Justice Department used to justify the FBI's extraordinary search of the former President's Florida home as part of an investigation into obstruction of justice and mishandling classified material that could put national security at risk.

Investigators argued that they needed to conduct the search after they found classified materials in boxes already recovered from Mar-a-Lago -- including files that could compromise "clandestine human sources" or overseas intelligence-gathering tactics if they were disclosed.

"There is probable cause to believe that additional documents that contain classified (National Defense Information) or that are Presidential records subject to record retention requirements currently remain at (Mar-a-Lago)," the FBI affidavit says. "There is also probable cause to believe that evidence of obstruction will be found at (Mar-a-Lago.)"

The Justice Department sought the warrant after the National Archives engaged in a protracted months-long effort to retrieve documents from Trump's White House that were being stored at Mar-a-Lago. After the Archives organized the return of 15 boxes of presidential materials from Mar-a-Lago in January, it referred the matter to the Justice Department for a criminal investigation.

FBI agents reviewed the 15 boxes provided to the National Archives in May, and the affidavit details the amount of classified material that was found.

In the affidavit, the Justice Department said there were "184 unique documents bearing classification markings, including 67 documents marked as CONFIDENTIAL, 92 documents marked as SECRET, and 25 documents marked as TOP SECRET."

Threats to witnesses

The Justice Department also released a redacted legal brief explaining why it proposed the redactions to the affidavit, including possible threats to witnesses.

The DOJ argued that, without the proposed redactions, "the affidavit could be used to identify many, if not all, of these witnesses." What follows is two paragraphs of redacted material.

"If witnesses' identities are exposed, they could be subjected to harms including retaliation, intimidation, or harassment, and even threats to their physical safety," the filing said. "As the Court has already noted, 'these concerns are not hypothetical in this case.'"

Reiterating language prosecutors previously used to describe why the affidavit should be kept secret, the DOJ's legal brief said its details would provide a "road map" to the investigation and that revealing "this information could thus adversely impact the government's pursuit of relevant evidence."

It appears that one example of this risk is laid out in a redacted paragraph.

"In addition, revealing this information could severely disadvantage the government as it seeks further information from witnesses," the filing said. "In short, the government has well-founded concerns that steps may be taken to frustrate or otherwise interfere with this investigation if facts in the affidavit were prematurely disclosed."

The sworn affidavit released Friday was written by an FBI special agent, whose identity was redacted to protect them from potential violence and threats. The document does reveal the agent was trained in "counterintelligence and espionage investigations" at the FBI Academy in Quantico, Virginia, and has expertise investigating people who "unlawfully collect, retain, and disseminate sensitive government information."

Classified markings

The affidavit also says that there were markings on the documents with multiple classified compartmentalized controls. "Based on my training and experience, I know that documents classified at these levels typically contain" national defense information, wrote the special agent who authored the affidavit.

"Several of the documents also contained what appears to be (the former President)'s handwritten notes," the affidavit says.

The FBI search of Mar-a-Lago on August 8 occurred two months after a trip made by top department officials, where they were shown where Trump was storing some of the materials. In the time between, investigators became suspicious members of Trump's team weren't being fully truthful about the situation and that documents were being withheld in the efforts to return the records to the federal government.

FBI used separate team to search Trump's office to protect against privilege issues

The FBI used law enforcement personnel who were not part of the investigation to search Trump's office in order to protect against potential attorney-client privilege issues, according to the affidavit.

The affidavit unsealed Friday says that the FBI used a "Privilege Review Team" to search the "45 office," separate from the investigators who searched other areas of Trump's residence authorized by the warrant.

"The Privilege Review Team will search the '45 Office' and conduct a review of the seized materials from the '45 Office' to identify and segregate documents or data containing potentially attorney-client privileged information," the affidavit says.

The affidavit says that if the review team determined there were "documents are potentially attorney-client privileged or merit further consideration in that regard," the team could take steps to seek a court determination, keep the documents from the investigative team, or "disclose the document to the potential privilege holder."

Fight over releasing the affidavit

The affidavit was released after a fight in court over what level of transparency the public was owed into a search with the historic significance of one involving the home of a former president. Soon after news of the search broke, news outlets, including CNN, and other entities filed in court, seeking the release of the warrant materials.

The Justice Department was initially willing to release some of the warrant documents publicly, with Attorney General Merrick Garland telling reporters earlier this month that the Trump team's public confirmation of many aspects of the search made the move appropriate in the face of the DOJ's usual habit of keeping such materials secret.

Prosecutors balked at releasing the warrant affidavit itself, which they said would provide a "road map" to the investigation and chill the cooperation of witnesses in this and other probes. They also argued that once the necessary redactions were made, the document would be devoid of meaning.

But US Magistrate Judge Bruce Reinhart -- who approved the warrant in early August and presided over the document release dispute -- did not buy that argument. Under his instruction, the DOJ instead proposed redactions, which he found acceptable, prompting his order for the release.

Trump calls for document's release but sits out court back-and-forth

Trump has publicly called for its release as he baselessly claimed that he was the target of a "witch hunt."

But his attorneys did not make any formal move to weigh in on the dispute before Reinhart. Only two weeks after the search did his legal team raise objections to it in court -- but in a separate legal action filed that landed before a different judge in the Southern District of Florida.

In that lawsuit, Trump is asking for a third party known as a "special master" to oversee the FBI's review of the materials it seized at Mar-a-Lago. His filing this week referenced a desire to see the affidavit in full, but he didn't request an order from the judge to do so. Other apparent legal shortcomings in the complaint prompted the judge, Trump-appointee Aileen Cannon, to order he make new submissions by Friday midnight laying out exactly what he wanted and why she had the authority to grant it.

The quick pace of the proceedings around learning more about the FBI's search has showcased the disarray in Trump's legal response to the investigation. The narrative that Trump and his allies have put forward about his handling of the documents in their PR response to the search has not matched what Trump's legal team claimed in the private negotiations with the Archives that started a year and a half ago, according to documents that have been made public from those conversations.

This story has been updated with additional details.