A man looks down at his smartphone as he walks past the offices of the Associated Press in Manhattan, New York (Reuters)

Media organisations and press freedom watchdogs have condemned the seizure of thousands of Associated Press (AP) phone call records by the US Department of Justice.

AP said the Justice Department secretly obtained two months worth of telephone records of its reporters and editors, in what is believed to be an attempt to track down the news agency's sources behind an alleged Yemen terrorist plot story.

Reporters Without Borders called the seizure an "extremely grave violation of freedom of information".

"We think that such a flagrant violation of constitutional guarantees needs to be the subject of a congressional commission of enquiry," Reporters Without Borders secretary-general Christophe Deloire said.

"We regret to see that the federal government has not ended the practices that prevailed during President George W. Bush's two terms, when officials sacrificed the protection of private data and, above all, the First Amendment right to be informed."

AP lawyers said the Justice Department obtained from phone companies the records for some 100 journalists using more than 20 separate telephone lines between April and May 2012, without notifying the news agency in advance.

The records listed outgoing calls for work and personal phone numbers of individual reporters, general AP office numbers in New York, Washington and Hartford, Connecticut, and the main number for the AP in the House of Representatives press gallery.

It was not clear if the records also included incoming calls or duration of the calls.

AP CEO Gary Pruitt said authorities committed a "massive and unprecedented intrusion" into how news organizations gather news.

"There can be no possible justification for such an overbroad collection of the telephone communications of The Associated Press and its reporters.

"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 wrote in a letter of protest sent to Attorney General Eric Holder.

Pruitt demanded the return of the phone records and destruction of all copies.

The department of Justice said it issued subpoenas for phone records but only after it made "every reasonable effort to obtain information through alternative means" as prescribed by law.

"We must notify the media organization in advance unless doing so would pose a substantial threat to the integrity of the investigation," the department of Justice said.

"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."

AP said the government would not say why it sought the records but it is likely the seizure was related to a May 7, 2012 article about a CIA operation in Yemen that stopped an al-Qaida plot to detonate a bomb on an airplane bound for the US.

The publication was followed by the opening of a justice department investigation on the information leak. CIA Director John Brennan said he was questioned by the FBI as a possible source

Phone records for five reporters and an editor who were involved in the story were among those seized.

"This is really a disturbing affront to a free press. It's also troubling because it is consistent with perhaps the most aggressive administration ever against reporters doing their jobs - providing information that citizens need to know about our government," said Arnie Robbins, executive director of the American Society of News Editors.

"The attorney general must explain the Justice Department's actions to the public so that we can make sure this kind of press intimidation does not happen again," said Laura Murphy, director of The American Civil Liberties Union Washington legislative office.

The White House denied any involvement in the incident. "We are not involved in decisions made in connection with criminal investigations, as those matters are handled independently by the Justice Department," spokesman Jay Carney said.