Chip Somodevilla / Chip Somodevilla / Getty Images file

Attorney General Eric Holder agreed to a review of Justice Department guidelines for investigations involving journalists, President Barack Obama said Thursday.

The Justice Department pledged Friday to to review its policies relating to the seizure of information from journalists after acknowledging that a controversial search warrant for a  Fox News reporter’s private emails  was approved “at the highest levels” of the Justice Department, including “discussions” with Attorney General  Eric Holder.

The statement, confirming an NBC News account of Holder’s role, defended the secret warrant to obtain reporter James Rosen’s emails as a legitimate step to obtain evidence as part of an investigation of Stephen Kim. A former intelligence analyst, Kim has since been indicted under the Espionage Act for leaking classified information to Rosen about North Korea. He has denied the charges.

In a 2010 affidavit in support of the search warrant, an FBI agent named Rosen as a possible “co-conspirator” in the case because he “asked, solicited and encouraged” Kim to give him information.

“After extensive deliberations, and after following all applicable laws, regulations and policies, the Department sought an appropriately tailored search warrant under the Privacy Protection Act,” said a department official, referring to a federal law that governs under what circumstances information can be subpoenaed from the news media. “And a federal magistrate judge made an independent finding that probable cause existed to approve the search warrant.”

Nevertheless, said the official, who spoke on condition of anonymity, Holder “understands the concerns that have been raised by the media and has initiated a re-evaluation of existing department policies and procedures.” The official said the department must strike “the appropriate balance” between preventing leaks of classified information and “First Amendment rights,”adding that passage of a new media shield law “and appropriate updates to the department”s internal guidelines” will help achieve that.  

 The statement comes  amid a firestorm of criticism from news media groups over the Rosen search warrant and a secret subpoena for the phone records of AP reporters. It also comes one day after President Obama addressed the issue in a major speech on counter-terrorism policy, saying "I am troubled by the possibility that leak investigations may chill the investigative journalism that holds government accountable," Obama said. "Journalists should not be at legal risk for doing their jobs."

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Holder previously said he recused himself from the AP subpoena because he had been questioned as a witness in the underlying investigation into a leak about a foiled bomb plot in Yemen. His role in personally approving the Rosen search warrant had not been previously reported until NBC News reported it on Thursday.

A law enforcement official. who also spoke on condition of anonymity, said Holder's approval of the Rosen search, in the spring of 2010, came after senior Justice officials concluded there was "probable cause" that Rosen's communications with Kim met the legal burden for such searches. 

In an affidavit in support of a search warrant to Google for Rosen's emails, an FBI agent wrote that the Fox News journalist -- identified only as "the Reporter" -- had "asked, solicited and encouraged Mr. Kim to disclose sensitive United States internal documents and intelligence information." 

"The Reporter did so by employing flattery and playing to Mr. Kim's vanity and ego,” it continued. “Much like an intelligence officer would run a clandestine intelligence source, the Reporter instructed Mr. Kim on a covert communications plan that involved" emails from his gmail account.

The affidavit states that FBI agents had tracked Rosen’s entrances and exits of the State Department in order to show that they had coincided with Kim’s movements. Based on that and other findings, the affidavit by FBI Agent Reginald B. Reyes, stated, “There is probable cause to believe that the Reporter has committed a violation” of the Espionage Act “at the very least, either as an aider, abettor and/or co-conspirator of Mr. Kim.”

It also said that Google was specifically instructed not to notify “the subscriber” -- Rosen -- that his emails were being seized.

In new documents disclosed Thursday, the Justice Department sought and obtained approval to keep the search warrant, which was approved by a federal magistrate, under seal. It was unsealed in November 2011, but never made a part of the docket of Kim’s case and went unnoticed until this week.

Justice officials have since said they do not intend to criminally charge Rosen, but media groups have condemned the issuance of the search warrant itself.

"The Justice Department's decision to treat routine newsgathering efforts as evidence of criminality is extremely troubling and corrodes time-honored understandings between the public and the government about the role of the free press," said Bruce Brown, executive director of the Reporters Committee for Freedom of the Press.

In his speech Thursday, Obama reiterated his determination to pursue leak investigations. "We must enforce consequences for those who break the law and breach their commitment to protect classified information," he said.

  But, he said, "Our focus must be on those who break the law," not journalists. He said he was calling on Congress to pass a media shield law and had raised the issue with Holder, "who shares my concern."

As part of the Justice Department review of guidelines, the president said, Holder will convene a group of media organizations to hear their views and “report back to me by July 12th."

NBC News Chief Justice Correspondent Pete Williams contributed to this report.

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This story was originally published on Thu May 23, 2013 5:16 PM EDT

US Air Force via Reuters

A Predator drone is shown in an undated photo from the Air Force.

Michael Reynolds / EPA

U.S. Attorney General Eric Holder addresses the National Association of Attorneys General in Washington, D.C., on Feb. 26.

The Obama administration has "no intention" of carrying out drone strikes against suspected terrorists in the United States, but could use them in response to “an extraordinary circumstance” such as the 9/11 terror attacks, according to a letter from Attorney General Eric Holder obtained by NBC News.

Sen. Rand Paul, R-Ky., who received the March 4 letter from Holder, called the attorney general’s refusal to rule out drone strikes in the U.S. “more than frightening.” 

The letter from Holder surfaced just as the Senate Intelligence Committee was voting 12-3 to approve White House counterterrorism adviser John Brennan to be CIA director. The vote came after the White House agreed to share additional classified memos on targeted drone strikes against U.S. citizens overseas.

Paul had threatened to hold up Brennan's confirmation on the floor of the Senate if the administration did not clarify whether targeted drone strikes could be used inside the U.S.

In his letter, Holder called the question of drone strikes inside the U.S. "entirely hypothetical, unlikely to occur and we hope no president will ever have to confront. … As a policy matter, moreover, we reject the use of military force where well-established law enforcement authorities in this country provide the best means for incapacitating a terrorist threat."

But Holder then appeared to leave the door open to such strikes in extreme circumstances.

Read the full letter

"It is possible, I suppose, to imagine an extraordinary circumstance in which it would be necessary and appropriate under the Constitution and applicable laws of the United States for the president to authorize the military to use lethal force within the territory of the United States. For example, the president could  conceivably have no choice but to authorize the military to use such force if necessary to protect the homeland in the circumstances of a catastrophic attack like the ones suffered on Dec. 7, 1941 and Sept. 11, 2001." 

In a statement, Paul said, “The U.S. attorney general’s refusal to rule out the possibility of drone strikes on American citizens and on American soil is more than frightening – it is an affront the Constitutional due process rights of all Americans.” 

Paul told NBC News that the response by Holder could lead to a situation where “an Arab-American in Dearborn (Mich.) is walking down the street emailing with a friend in the Mideast and all of a sudden we drop a drone” on him. He said it was “really shocking” that President Barack Obama, a former constitutional law professor, would leave the door open to such a possibility.

Paul said he will filibuster Brennan’s confirmation over the issue but acknowledged “we probably can’t stop him.” He did say, however, he intends to co-sponsor a bill with Republican Sen. Ted Cruz of Texas, to be introduced in the next few days, that would bar the president from using drone strikes in the U.S.

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U.S. Border Patrol agent Brian A. Terry was killed during a shootout with Mexican bandits south of Tucson, Ariz., in December 2010. Weapons seized afterward were later linked to Operation Fast and Furious, an ATF effort to trace the flow of weapons to Mexican drug cartels.

A long-awaited report on the U.S. government’s controversial gun-trafficking operation known as “Fast and Furious” released Wednesday found no evidence that Attorney General Eric Holder knew of the botched effort to trace the flow of guns to Mexico’s drug cartels prior to its public unraveling in January 2011. 

The report by the Justice Department’s Inspector General Michael Horowitz said there is "no evidence that ... Holder was informed about Operation Fast and Furious, or learned about the tactics employed by ATF in the investigation" before Congress began pressing him for information about it in early 2011.

The inspector general did determine that the acting deputy attorney general, Gary Grindler, received a briefing about the ill-fated gun-tracing operation in March 2010, but that the briefing "failed to alert Grindler to problems in the investigation." 

The report also concluded that the operation was "seriously flawed and supervised irresponsibly" by federal officials in Arizona, who allowed it to continue in hopes of scoring a big case against a gun-trafficking organization despite obvious problems. 

No one in Arizona, at ATF headquarters in Washington or at the Justice Department acted to end the operation until two weapons that were allowed to flow into Mexico were found at the scene of a shootout where a federal border agent, Brian Terry, was killed in December 2010.

"Fast and Furious" was an attempt to trace the flow of guns from the US into Mexico.  ATF agents were instructed to allow suspected gun runners for the Mexican cartels to take guns into Mexico, because local ATF officials and local prosecutors believed they could then follow the weapons to the cartel higher-ups in Mexico.  It didn't work that way, and roughly 2,000 guns were lost, most of them AK-47-type rifles, the report said.

Even after two of the trafficked guns showed up at the scene of Terry's death, senior ATF leaders did little to find out what went wrong.  Instead, the report said, Kenneth Melson, then the acting ATF director, seemed more concern that agents were leaking information to the news media about the botched operation.

Read the full report

Holder, in a statement issued immediately after the report's release, said its "key conclusions are consistent with what I, and other Justice Department officials, have said for many months now," that senior Justice Department officials were unaware of the "flawed strategy and tactics" that dated back to the administration of George W. Bush and made no effort to "cover up information or mislead Congress about it."

Holder also announced that Melson, who was transferred out of the top job at the ATF last year, was retiring, effective immediately. A second Justice Department official, former Deputy Assistant Attorney General Jason Weinstein, has resigned. The report said Weinstein failed to tell Attorney General Holder about problems with the Fast and Furious operation. 

In all, 14 current federal employees were singled out in the report for potential disciplinary action.

The report's publication seemed to do little to end the bitter rivalry between Holder and Rep. Darrel Issa, the California Republican who was among the first to question the Fast and Furious operation.

 "It is unfortunate that some were so quick to make baseless accusations before they possessed the facts about these operations -- accusations that turned out to be without foundation and that have caused a great deal of unnecessary harm and confusion," Holder said in his statement.  

"I hope today's report acts as a reminder of the dangers of adopting as fact unsubstantiated conclusions before an investigation of the circumstances is completed," he said. 

In his own statement, Issa said, "Contrary to the denials of the attorney general and his political defenders in Congress, the investigation found that information in wiretap applications approved by senior Justice Department officials in Washington did contain red flags showing reckless tactics and faults Attorney General Eric Holder’s inner circle for their conduct.

 "It’s time for President Obama to step in and provide accountability for officials at both the Department of Justice and ATF who failed to do their jobs," Issa said.

Politically charged partisan dispute
The operation has become a politically charged partisan dispute heading into the November elections, with congressional Republicans charging that the Obama administration has withheld documents that would show the involvement of senior government officials, including Holder.

On June 28, the Republican-led House of Representatives voted to hold Holder in contempt of Congress for failing to disclose internal Justice Department documents in response to a subpoena – the first time that sanction has been imposed on a sitting member of a president’s Cabinet.

The department’s inspector general spent more than a year investigating the so-called “gun-walking” scandal  – in which agents of the federal Bureau of Alcohol, Tobacco, Firearms and Explosives, commonly known by the ATF acronym, in Arizona allow suspected gun runners to take guns into Mexico. The Fast and Furious operation was part of a broader initiative known as Project Gunrunner. 

Local ATF officials and local prosecutors believed they could then follow the weapons to the cartel higher-ups in Mexico.  It didn't work that way. Thousands of guns were lost and only lower-level straw buyers of the weapons were ever arrested. 

Two of the weapons turned up at the scene of a shootout where a federal border agent, Brian Terry, was killed on Dec. 14, 2010, near the Mexico border, though those guns were never tied directly to his death. 

A Mexican legislator, Humberto Benitez Trevino, claimed last year that weapons that crossed the border during the attempted sting have been linked to the deaths or wounding of at least 150 Mexican civilians, but did not provide any supporting documentation or say how that number was calculated.

Pete Williams is NBC News justice correspondent; NBC News Projects Editor Mike Brunker also contributed to this report.

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