WASHINGTON — A federal judge on Saturday ruled that John R. Bolton, President Trump’s former national security adviser, can go forward with the publication of his memoir, rejecting the administration’s request for an order that he try to pull the book back and saying it was too late for such an order to succeed.

“With hundreds of thousands of copies around the globe — many in newsrooms — the damage is done. There is no restoring the status quo,” wrote Judge Royce C. Lamberth of the Federal District Court of the District of Columbia.

But in a 10-page opinion, Judge Lamberth also suggested that Mr. Bolton may be in serious jeopardy of forfeiting his $2 million advance, as the Justice Department has separately requested — and that he could be prosecuted for allowing the book to be published before receiving final notice that a prepublication review process to ensure it had no classified information was complete.

“Bolton has gambled with the national security of the United States,” Judge Lamberth wrote. “He has exposed his country to harm and himself to civil (and potentially criminal) liability. But these facts do not control the motion before the court. The government has failed to establish that an injunction will prevent irreparable harm.”

The main elements of the book, “The Room Where It Happened,” an unflattering account of Mr. Trump’s conduct in office, have already been widely reported.

Judge Lamberth issued the ruling after holding a public hearing on Friday about the government’s request in which he had strongly signaled that he believed the Justice Department’s request for a temporary restraining order and preliminary injunction had come too late to ensure that any classified information in the book would remain secret.

Later on Friday, he held a closed-door hearing with government lawyers to discuss their contention that classified information remains in the manuscript — including an exceptionally restricted kind that could reveal closely held intelligence sources and methods — even though the National Security Council’s top official for prepublication review had told Mr. Bolton that she was satisfied with the edits he had made at her request.

After her review was complete, the White House never sent a final approval letter to Mr. Bolton. But he told Simon & Schuster to publish anyway. Meanwhile, without telling Mr. Bolton, the White House opened a second review by a National Security Council official, Michael T. Ellis, who claimed last week to have found at least six examples of classified information in the manuscript.

Mr. Ellis had not received training in prepublication review until after he analyzed Mr. Bolton’s manuscript. Charles Cooper, a lawyer for Mr. Bolton, has accused the administration of politicizing the process as a pretext to prevent his client from revealing embarrassing facts about Mr. Trump.

But other national security officials have also said in declarations to the court that they think classified information is in the book.

Judge Lamberth will also oversee the part of the lawsuit that seeks to seize Mr. Bolton’s proceeds for writing the book as a penalty for purportedly breaching the agreements he signed as a condition of receiving classified information to go through the prepublication review process. Mr. Cooper has argued that Mr. Bolton lived up to them.

The judge wrote that after viewing classified declarations and discussing them in the closed hearing, he was “persuaded that defendant Bolton likely jeopardized national security by disclosing classified information in violation of his nondisclosure agreement obligations.”

Judge Lamberth wrote that if Mr. Bolton was dissatisfied with the delay, he could have sued the government instead of unilaterally publishing. He said Mr. Bolton had gambled and lost.

“This was Bolton’s bet: If he is right and the book does not contain classified information, he keeps the upside mentioned above; but if he is wrong, he stands to lose his profits from the book deal, exposes himself to criminal liability, and imperils national security,” he wrote. “Bolton was wrong.”