WASHINGTON — Lawyers for the Justice Department and John R. Bolton, President Trump’s former national security adviser, clashed on Friday as a federal judge weighed a Trump administration request to order Mr. Bolton to somehow claw back his memoir even though hundreds of thousands of copies were printed and distributed around the world.

In a hearing conducted by telephone because of the pandemic, David M. Morrell, a Justice Department lawyer, said Mr. Bolton was in “flagrant breach” of his obligation to complete a prepublication review designed to ensure his book, “The Room Where It Happened,” has no classified information. The onus was on Mr. Bolton to make an effort to fix the mess, Mr. Morrell argued.

“Deterrence matters,” Mr. Morrell told the judge overseeing the case, Royce C. Lamberth of the Federal District Court of the District of Columbia. “There is a massive government interest that these agreements that are designed to protect classified information are not willy-nilly breached by disgruntled authors.”

But Charles J. Cooper, a lawyer for Mr. Bolton, called the request for an order that his client pull back the memoir “theater” both under the First Amendment and as a matter of practical reality. The Justice Department has also claimed that such an order could bind Mr. Bolton’s publisher, Simon & Schuster, and bookstores.

The main elements of the book, an unflattering account of Mr. Trump’s conduct in office, have already been widely reported.

“This really isn’t a judicial proceeding,” Mr. Cooper said. “This does not have as its first purpose actually convincing you to order John Bolton to do something that he is utterly powerless to do, and that you are therefore utterly powerless to force him to do.”

Judge Lamberth made no ruling on the request for a restraining order from the bench, and he said that before making any decision he needed to hold a second, closed-door hearing with only the government to discuss the details of information in the book the administration now says are classified.

He held the closed hearing later on Friday — in person because it involved discussion of classified information — according to a notation added to the case’s electronic docket.

The Justice Department sued Mr. Bolton on Tuesday, seeking to seize his proceeds from the memoir. It accused him of violating several agreements he had signed when taking the job to submit to the prepublication review process as a condition of receiving classified information. The Supreme Court has upheld the constitutionality of such seizures.

But a day later, the department significantly escalated its efforts by asking for a restraining order and injunction against Mr. Bolton to try to halt further distribution of his book. It also submitted a declaration by a National Security Council official, Michael T. Ellis, saying the manuscript contained classified information, including an exceptionally restricted category that could reveal intelligence sources and methods.

That escalation of the case into an 11th-hour attempt to stop further dissemination of the book raised not just practical questions but constitutional alarms. The Supreme Court has ruled that the First Amendment only rarely permits the government to gag speech. (A group of news organizations, including The New York Times, submitted a “friend of the court” brief arguing that such “prior restraint” on publication would be unconstitutional.)

The judge opened the hearing with a suggestion that he may be inclined to agree with Mr. Cooper about the request for an order. “The horse, as we used to say in Texas, seems to be out of the barn,” Judge Lamberth said.

But he also will be asked to decide other matters — like the government’s request to seize Mr. Bolton’s $2 million advance — and asked why Mr. Bolton had walked away from the prepublication review and did not tell the government that he had told Simon & Schuster to start printing.

Mr. Cooper, however, argued that Mr. Bolton had lived up to his obligations under the spirit and text of the agreements his client signed. He stressed that his client had worked with Ellen Knight, the National Security Council’s senior director for prepublication review, and made numerous changes at her request. She told him in late April that she had no more edits.

But the White House never sent a formal letter saying the process was complete — something Mr. Cooper argued was unnecessary under the version of the agreement his client signed — and it turned out that it had begun a second review by Mr. Ellis without telling Mr. Bolton until this month. Mr. Ellis submitted an affidavit this week claiming that he had found at least instances of six classified information in the book, including some from the exceptionally restricted category.

Mr. Cooper has portrayed Mr. Ellis’s intervention as politically motivated and illegitimate, and he made much of the government’s acknowledgment, in a revised complaint on Friday, that Mr. Ellis had received no training in how to review classified information until this month — after he had studied the manuscript and identified the material he said was classified even though Ms. Knight had not considered it to be.

The Justice Department did not submit an affidavit from Ms. Knight, as Judge Lamberth pointed out and Mr. Cooper also emphasized. But Mr. Cooper said that if the legal fight continues, he will seek to question her under oath.

Under questioning from Judge Lamberth, Mr. Morrell acknowledged that as many as half of the six examples Mr. Ellis flagged may not have been classified when Mr. Bolton wrote his manuscript, and only became so because Mr. Ellis deemed them as such. He also said he knew of no previous instance of senior officials starting a second review of a manuscript after the first reviewer made changes and was satisfied that it had no classified information.

But he said Mr. Ellis had access to information Ms. Knight did not, and argued that the circumstances — of a national-security official at the level of Mr. Bolton, writing about current policy matters just months after leaving and while the administration in which he served was still in office — were extraordinary, justifying an extra layer of review.

While the subject was serious, the hearing was interrupted by the sort of absurdities and difficulties that have become common in judicial proceedings conducted remotely during the pandemic.

At one point Judge Lamberth interrupted Mr. Morrell while the lawyer was on a roll to tell him that there was a problem with his image — the participants had video as well as audio — and Mr. Morrell began waving and asked if the judge could see his movement. At another point, a chime sounded and Mr. Cooper apologized and explained that someone had rung his doorbell.

Katie Benner contributed reporting.