Holder told a press conference he recused himself because he did not have all the facts related to the investigation of a leak involving a foiled al-Qaida plot in Yemen. Holder called the leak "very serious" and a Justice Department official said Holder stepped aside because he had been interviewed as part of the investigation, The Hill reported.
"It put the American people at risk, and that is not hyperbole. It put the American people at risk," Holder said of the leak.
Journalism groups and lawmakers expressed outrage over the phone records examination.
"The Justice Department's secret acquisition of two months of the business and personal phone records of AP's reporters and other employees is shameful and outrageous," Society of Professional Journalists President Sonny Albarado said in a statement emailed to United Press International.
"Attorney General Holder and President Obama have once again shown by their actions that their words about transparency and government openness are hollow," said Albarado, city editor at the Arkansas Democrat-Gazette in Little Rock.
The Newspaper Association of America said the department's "wholesale seizure of confidential telephone records" amounted to "unprecedented" actions that "shock the American conscience and violate the critical freedom of the press protected by the U.S. Constitution and the Bill of Rights."
House Speaker John Boehner, R-Ohio, said through a spokesman: "The First Amendment is first for a reason. If the Obama administration is going after reporters' phone records, they better have a damned good explanation."
House Oversight and Government Reform Committee Chairman Darrell Issa, R-Calif., linked the disclosure to a mushrooming controversy over revelations the Internal Revenue Service targeted Tea Party groups for heightened scrutiny and allegations the Obama administration misled the public about the nature of the Sept. 11, 2012, terrorist attacks on a U.S. diplomatic post in Libya.
"Coming within a week of revelations that the White House lied to the American people about the Benghazi attacks and the IRS targeted conservative Americans for their political beliefs, Americans should take notice that 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," Issa said.
Senate Judiciary Committee Chairman Patrick Leahy, D-Vt., said he was "very troubled by these allegations" and wanted to hear the government's explanation.
"The burden is always on the government when they go after private information -- especially information regarding the press or its confidential sources. I want to know more about this case, but on the face of it, I am concerned that the government may not have met that burden," Leahy said in a statement.
The outrage came after the news cooperative said Monday the Justice Department secretly obtained April and May 2012 records of outgoing calls from more than 20 phone lines of AP journalists -- including home and cellphone numbers -- sometime this year as part of a yearlong investigation into the disclosure of classified information about a failed 2012 al-Qaida plot.
The wire service said it was not told the reason for the seizure. But it said the timing and several journalists targeted, along with earlier congressional testimony, suggested the actions were tied to an AP story the CIA broke up a plot by al-Qaida's Yemeni affiliate to blow up a U.S.-bound passenger jet on the one-year anniversary of the May 2, 2011, killing of Osama bin Laden.
Five targeted reporters and an editor were involved in that May 7, 2012, story.
The AP delayed reporting the story at the request of U.S. officials who said it would jeopardize national security. Once the officials said those concerns were over, AP reported the plot, even though the Obama administration asked AP to continue holding the story until the administration could make an official announcement, the news service said.
AP President Gary Pruitt said in a letter to Holder the seizure was a "massive and unprecedented intrusion" into AP's newsgathering activities.
"There can be no possible justification for such an overbroad collection of the telephone communications of the Associated Press and its reporters," he wrote. "These records potentially reveal communications with confidential sources across all of the newsgathering activities undertaken by the AP during a two-month period, provide a road map to AP's newsgathering operations, and disclose information about AP's activities and operations that the government has no conceivable right to know."
Pruitt demanded the government return the phone records and destroy all copies.
Under Obama, six current and former government officials have been indicted in leak-related cases, twice the number brought under all previous administrations combined.
Usually when investigators seek information about a news organization's source, the organization moves to quash a subpoena for its records. But in this case, AP was not aware the records had been obtained.
"We must notify the media organization in advance unless doing so would pose a substantial threat to the integrity of the investigation," U.S. Attorney for the District of Columbia Ronald Machen said through a spokesman.
Machen was assigned by Holder last June to lead one of two major leak investigations.
"Because we value the freedom of the press," spokesman Bill Miller said, "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."
Justice Department guidelines require subpoenas of news organization records to be personally approved by the attorney general. It was not immediately clear if those guidelines were followed in this case.
Holder's office did not immediately respond to requests for comment.
White House spokesman Jay Carney said late Monday the White House was not involved in the AP subpoenas.
"Other than press reports, we have no knowledge of any attempt by the Justice Department to seek phone records of the AP," he said. "We are not involved in decisions made in connection with criminal investigations, as those matters are handled independently by the Justice Department."
It was not immediately clear if a judge or grand jury signed off on the subpoenas.
A federal grand jury in Washington has been investigating the possible leak of classified information to the AP for several months, The Washington Post reported.