The Associated Press has revealed that it's been notified by the Justice Department that investigators obtained records on more than 20 phone lines used by AP reporters and editors last April and May. NBC's Pete Williams reports.

WASHINGTON -- The Justice Department used a secret subpoena to obtain two months of phone records for Associated Press reporters and editors without notifying the news organization, a senior department official tells NBC News, saying the step was necessary to avoid "a substantial threat to the integrity" of an ongoing leak investigation.

Michael Isikoff, NBC News national investigative correspondent, talks with Rachel Maddow about the Justice Department's disclosure that it has seized two months of phone records of many AP reporters, apparently in pursuit of the source of a leak about an al Qaeda bomb plot in Yemen.

The seizure of the phone records, disclosed earlier Monday by AP President and CEO Gary Pruitt, is the latest move in a series of high profile and controversial investigations of leaks of classified information by the Justice Department. In a letter of protest to Attorney General Eric Holder, Pruitt said obtaining more than two months of AP phone records on 20 separate telephone lines without prior notice was a "massive and unprecedented intrusion" into news-gathering operations.

It also drew a swift rebuke Monday from members of Congress and freedom of the press watchdogs, one of whom called the move "Nixonian."

Ronald C. Machen, Jr., the U.S. attorney in Washington, D.C., revealed in a letter to the AP on Friday that federal prosecutors obtained the records. The letter did not give a reason for obtaining the records, but Machen is conducting an investigation into the leak of classified information about a foiled terror plot in Yemen last year. An AP story last spring reported details of a CIA operation in Yemen that stopped an al Qaeda plot to detonate a bomb on an airplane bound for the United States.

In his letter to Holder, Pruitt said the seized phone records were from early 2012 and included phone lines for AP bureaus in New York, Washington DC, Hartford, Connecticut and the AP line at the House of Representatives. He said the records seized also included those from the home phones and cell phones of individual journalists.

"We regard this action by the Department of Justice as a serious interference with AP's constitutional rights to gather and report the news," Pruitt said.

Associated Press Executive Editor Kathleen Carroll calls the Justice Department's actions to be "very distressing."

Holder last June appointed Machen to conduct the investigation of the Yemen terror plot leak and Rod Rosenstein, the U.S. attorney in Maryland, to oversee a separate probe into the leak of U.S. government efforts to use the Stuxnet computer virus to thwart the Iranian nuclear program. In later Senate testimony, Holder said that he and FBI director Robert Mueller had both been interviewed by FBI agents as part of the investigations because they had prior knowledge of the information that was leaked. (Under Justice regulations, any subpoena for news media phone records requires the "express authorization" of the attorney general. But a Justice Department spokeswoman did not respond Monday night when asked whether the attorney general had recused himself in the investigation.)

As another sign of the sensitivity of the case, CIA Director John Brennan disclosed earlier this year that he also had been questioned by FBI agents as part of the Yemen probe, but said he was later notified that he was not a subject of the investigation.

Bill Miller, spokesman for Machen, said in an email that the subpoena for the records was done by the book.

"Consistent with DOJ regulations, the department provided notification to the Associated Press of the receipt of toll records in a letter dated May 10, 2013," He noted that Justice regulations "do not require notification to the media prior to the issuance of legal process to obtain toll records."

In a separate email, Miller wrote: "We take seriously our obligations to follow all applicable laws, federal regulations, and Department of Justice policies when issuing subpoenas for phone records of media organizations. Those regulations require us to make every reasonable effort to obtain information through alternative means before even considering a subpoena for the phone records of a member of the media. We must notify the media organization in advance unless doing so would pose a substantial threat to the integrity of the investigation.

"Because we value the freedom of the press, we are always careful and deliberative in seeking to strike the right balance between the public interest in the free flow of information and the public interest in the fair and effective administration of our criminal laws.”

The regulations cited by Miller state that subpoenas for the news media in criminal cases should be done only when there are “reasonable grounds to believe … that a crime has occurred” and that the records sought are “essential to a successful investigation.” They also state that subpoenas should, wherever possible, “be directed at material information regarding a limited subject matter and “should cover a reasonably limited period of time and … avoid requiring production of a large volume of unpublished material.”

Since President Barack Obama took office, the Justice Department has aggressively pursued leak investigation and brought more criminal prosecutions – six in five years – than any previous administration. Those cases, which also have been sharply criticized by press groups, have also targeted reporters’ phone records: James Risen, a national security reporter for the New York Times, had his phone, credit card and bank records subpoenaed as part of a Justice Department prosecution of a former CIA officer accused of leaking classified information on Iran’s nuclear program to him.

But critics say the extensive nature of the subpoena for the AP phone records goes far beyond what was seen in earlier cases.

Rep. Darrell Issa, R-Calif., and chairman of the House Oversight and Government Reform Committee, vowed to investigate.

"This is obviously disturbing," he said. Coming in the wake of other disclosures about the administration’s response to the attack on the U.S. consulate in Benghazi, Libya, and the IRS’s targeting of conservative nonprofit groups, he said it showed "top Obama administration officials increasingly see themselves as above the law and emboldened by the belief that they don't have to answer to anyone."

Sen. Patrick Leahy, D-Vt., and chairman of the Senate Judiciary Committee, said he wanted to know more about the justification for the secret subpoena.

"The burden is always on the government when they go after private information -- especially information regarding the press or its confidential sources,” he said. “… I am concerned that the government may not have met that burden. I am very troubled by these allegations and want to hear the government's explanation."

Anti-secrecy watchdogs also criticized the move.

"I've never heard of a dragnet collection effort against a media organization like this," said Stephen Aftergood, who tracks secrecy issues for the Federation of American Scientists. "This was not a targeted monitoring of an individual reporter. It's a sweeping collection of an entire bureau's communications."

"The Justice Department’s seizure of the Associated Press’ phone records is Nixonian," said Danielle Brian, executive director of the Project on Government Oversight, a group that advocates on behalf of whistleblowers. "The American public deserves a full accounting of why and how this could happen."

NBC News' Capitol Hill Correspondent Kelly O'Donnell contributed to this report.

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