The Obama administration's crackdown on leaks could have chilling implications for the journalists who cover the White House. NBC's Michael Isikoff reports.

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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