The Obama administration has opened up a new front in its battle against media freedom by seizing phone records from the offices of the Associated Press news agency in what appeared to be an effort to track down the source who disclosed an alleged Yemen terrorist plot story.

The US attorney's office for the District of Columbia confirmed on Monday that subpoenas had been issued for phone records. It said it valued press freedom but it had to balance this against the public interest.

AP revealed on Monday that the justice department, without informing the organisation in advance, had obtained two months' worth of phone records of calls made by reporters and editors.

Lawyers for AP said the records, which the justice department appears to have obtained from the phone companies earlier this year, listed every call made by about 100 reporters from AP's main offices in New York, Washington and Hartford, Connecticut, and from its office in the House of Representatives press gallery between April and May last year. The justice department informed AP last Friday. AP described it as a "massive and unprecedented intrusion" into newsgathering operations.

The attorney's office refused to say why the seizure had been made but it is almost certainly in relation to an AP exclusive report on 7 May last year in which it reported the CIA had stopped a plot by an al-Qaida affiliate in Yemen to destroy a US-bound airliner.

AP at the time agreed to White House and CIA requests to hold back publication because they said an intelligence operation was still under way. After being satisfied that these concerns had been met, AP published on the Monday, ignoring a request from the Obama administration to wait until Tuesday for the official announcement.

The justice department has since launched an investigation into the leak. The phone records of five of the reporters plus an editor involved in the Yemen story were among those taken.

AP's president and chief executive officer, Gary Pruitt, sent a letter of protest to the attorney-general, Eric Holder. "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 said.

He described it as "serious interference with AP's constitutional rights to gather and report the news".

Although Obama was elected on a liberal ticket in 2008 and again in 2012, his administration has mounted a sustained campaign through the courts and other means against whistleblowers, particularly in relation to what it claims are sensitive intelligence matters.

Media organisations and civil rights groups complain that many of the cases it appear to have to do with administrative secrecy than matters of national security.

The Obama administration has brought six cases against people suspected of leaking classified information, which AP described as being more than under all previous presidents combined.

A former CIA officer found himself in trouble for revealing details to journalists about waterboarding while a former member of the National Security Agency was prosecuted for disclosing that the agency was about to spend millions of dollars on a software programme that he argued was more expensive than a similar programme developed in-house.

The justice department, in its statement, defended the AP seizure. "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," it said.

The justice department said that it had, as required by law, made every reasonable effort to obtain the information through alternative means. Normally too, it would have had to notify the media in advance unless, as in this case, "doing so would pose a substantial threat to the integrity of the investigation".

The White House denied it had been involved in the justice department move or had any knowledge of it, insisting there was a separation between the executive and the judicial branches of government.

Jay Carney, the White House press spokesman, who was travelling with Obama on a Democratic fund-raising trip to New York, said: "Other than press reports, we have no knowledge of any attempt by the justice department to seek phone records of the AP. We are not involved in decisions made in connection with criminal investigations, as those matters are handled independently by the justice department. Any questions about an ongoing criminal investigation should be directed to the department of justice."

The CIA director, John Brennan, in February described the Yemen story as "an authorised and dangerous disclosure of classified information" and that disclosure was "irresponsible".

The alleged plot, apparently aimed to coincide with the first anniversary of the killing of Osama bin Laden, contradicted a claim by the Obama administration earlier that it had no knowledge of any plans for attacks to mark the anniversary.