WASHINGTON — White House aides improperly intervened to prevent a manuscript by President Trump’s former national security adviser John R. Bolton from becoming public, a career official said in a letter filed in court on Wednesday, accusing them of making false assertions and trying to coerce her to join their efforts, and suggesting that they retaliated when she refused.

In an extraordinary 18-page document, a lawyer for the official who oversaw the book’s prepublication review, Ellen Knight, portrays the Trump administration as handling its response to the book in bad faith. Her account implied that the Justice Department may have told a court that the book contains classified information — and opened a criminal investigation into Mr. Bolton — based on false pretenses.

An aide to Mr. Trump also “instructed her to temporarily withhold any response” to a request from Mr. Bolton to review a chapter on Mr. Trump’s dealings with Ukraine so it could be released during the impeachment trial, wrote Ms. Knight’s lawyer, Kenneth L. Wainstein.

He said that his client had determined in April that Mr. Bolton’s book, “The Room Where It Happened,” no longer contained any classified information, but the “apolitical process” was then “commandeered by political appointees for a seemingly political purpose” to go after Mr. Bolton. The actions she was asked to take were “unprecedented in her experience,” the letter said.

Ms. Knight said that political appointees repeatedly asked her to sign a declaration to use against Mr. Bolton that made a range of false assertions. She said that after her refusal, she was reassigned from the White House despite earlier expectations that she would transition to a permanent position there.

“She had never previously been asked to take the above-described measures, and she has never heard that predecessors in her position ever received such instructions in the course of their prepublication reviews,” the letter said.

Representatives for the National Security Council and the Justice Department did not immediately respond to requests for comment. A lawyer for Mr. Bolton, Charles J. Cooper, declined to comment on the specifics of the letter but said his client had not asked Ms. Knight to disclose her account of events and that he had received a copy of the letter unexpectedly on Tuesday evening.

The filing was an extraordinary twist in the legal saga surrounding Mr. Bolton’s book. The Trump administration unsuccessfully sought to block distribution of the book earlier this year after it was already printed, claiming despite Ms. Knight’s assessment that it contained large amounts of classified information. It is moving to seize his $2 million advance and has opened a criminal investigation, threatening criminal charges for unauthorized disclosures of secrets.

But the letter called into question the premise of all of those efforts — that the book, in its published form, contains any classified information.

Ms. Knight’s account is also the latest in a series of disclosures by current and former executive branch officials as the election nears accusing the president and his political appointees of putting his personal and political goals ahead of the public interest and an evenhanded application of the rule of law.

Mr. Wainstein recounted a series of irregularities that he said were unlike any other prepublication review Ms. Knight had handled in her two years working at the National Security Council.

Ms. Knight, after extensive work with Mr. Bolton to change aspects of his draft to eliminate classified information, had told his team informally that it no longer had any unpublishable material. But the White House never sent a formal letter saying the process was over and political appointees in the White House directed Ms. Knight not to communicate with them in writing about the book.

In June, as the delay dragged on, Mr. Bolton and Simon & Schuster published the book, arguing that Ms. Knight’s informal assurance fulfilled the legal commitment he had undertaken, as a condition of receiving his security clearance, to submit future writings about his job to prepublication review.

But the White House had earlier proceeded to have a politically appointed lawyer — Michael Ellis, a former aide to Representative Devin Nunes, Republican of California and a close Trump ally — conduct his own review of the book.

Mr. Ellis had no training in prepublication reviews at the time — he underwent it after he completed his review — and pronounced the book replete with still-classified information, a position the Justice Department then made in court seeking to block Mr. Bolton from distributing the book.

Mr. Ellis was wrong, Mr. Wainstein wrote. Rather than evaluating the book by prepublication review standards for writings by a private citizen, he essentially treated the manuscript as a government document being subject to a classification review.

The two are very different, the letter explained, on matters like discussing a phone call between a president and a foreign leader. Mr. Bolton’s book contains numerous accounts of such discussions between Mr. Trump and his counterparts.

While an official record of that call would be presumptively classified in its entirety, if the White House press secretary has disclosed the fact of that call and put aspects of what was discussed into the public domain, the prepublication review standards would not flag a manuscript’s similar discussion of such a call as classified and unpublishable.

“Mr. Ellis failed to analyze whether the information he marked as classified was still, in fact, classified and subject to redaction,” Mr. Wainstein wrote. “In determining the publishability of information in the manuscript, Mr. Ellis apparently focused on whether that same information could be found in classified government records. If he saw information in the manuscript that was also reflected in a classified government record, he appeared to have automatically deemed that information classified.”

The letter called into question a statement made by the judge who in June rejected the Justice Department’s request for an order blocking distribution of the already-printed book. The judge, Royce C. Lamberth of the Federal District Court of the District of Columbia, wrote in his ruling that it appeared the book contained large amounts of classified information and suggested that Mr. Bolton was likely to face civil and possibly criminal penalties.

But the letter noted that during his review, Judge Lamberth had looked at “the unchallenged declarations of N.S.C. official Michael Ellis and four presidentially appointed intelligence officials who reviewed passages of the manuscript in isolation and opined that they contained classified information, without any insight into the multilayered analysis and context that led Ms. Knight and her staff to determine that they did not.”

The letter also describes a behind-the-scenes pressure campaign that Mr. Trump’s appointees mounted against Ms. Knight in an effort to get her to say she had been wrong and the book still had classified information, as they prepared to ask for a judicial order blocking it.

On June 13, the letter said, politically appointed White House officials — led by Patrick Philbin, the deputy White House counsel — called her in for a Saturday meeting and challenged her on why she had signed off on large amounts of material that Mr. Ellis claimed was classified. By her account, she was able to explain why he was wrong about everything, frustrating them.

“It was clear to Ms. Knight that they were trying to get her to admit that she and her team had missed something or made a mistake, which mistake could then be used to support their argument to block publication,” it said. “To their consternation, Ms. Knight was able to explain the clear and objective reasoning behind her team’s decision-making as to each of the challenged passages.”

Over the next five days, the letter continued, a series of White House and Justice Department political appointees pressured her during 18 hours of meetings to sign an affidavit they could submit to a court for the litigation against Mr. Bolton that purported to describe her role in the process but was worded in a way that would support their narrative that her review was subpar and had left classified information in the book. She refused.

Ms. Knight — who was nearing the end of a two-year detail from the National Archives and Records Administration to the National Security Council — had expected up to that point that she would transition to a permanent position at the National Security Council. However, following the dispute over the Bolton book, she was instead sent back to the National Archives last month.

The allegations in Ms. Knight’s letter could dominate a hearing scheduled for Thursday in the civil dispute between the government and Mr. Bolton.

Nearly every Justice Department official in the civil division who signed the original complaint against Mr. Bolton has quit. The remaining civil lawyer on the complaint, Alexander Haas, will not argue for the government before the court. The department has given the case to Jennifer Dickey, who joined the department during the Trump administration and worked for a year in the White House Counsel’s Office on labor policy issues.

Mr. Bolton’s book presents an unflattering account of Mr. Trump’s conduct in office, including providing new evidence supporting the accusations that led to his impeachment by House Democrats but acquittal by Senate Republicans: that he abused his power over the nation’s foreign policy to try to obtain personal political benefits.

Mr. Trump has accused Mr. Bolton of lying while openly pressing the Justice Department to prosecute his former aide for spilling secrets, writing on Twitter that Mr. Bolton “broke the law by releasing Classified Information (in massive amounts). He must pay a very big price for this, as others have before him. This should never to happen again!!!”

In the letter’s account of the pressure brought on Ms. Knight to provide a statement the Justice Department could use against Mr. Bolton in litigation, she asked the lawyers why they were so insistent on pursuing legal action and speculated that the litigation was happening “because the most powerful man in the world said that it needed to happen.”

“Several registered their agreement with that diagnosis of the situation,” the letter said.

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