Washington (CNN) -- The Justice Department's sweeping collection of Associated Press phone records as part of a national security leak investigation has had a chilling effect on sources, the news agency's top executive said on Wednesday.
"Some of our long-trusted sources have become nervous and anxious about talking to us -- even on stories that aren't about national security," AP Chief Executive and President Gary Pruitt said at the National Press Club.
"In some cases, government employees that we once checked in with regularly will no longer speak to us by phone and some are reluctant to meet in person," he said.
The Justice Department subpoenaed and subsequently obtained two months of AP phone records as part of an investigation of its May 2012 coverage of a foiled airline bomb plot in Yemen.
Toll records would show what numbers were dialed from the AP lines and what numbers dialed in, but would not provide any information on the content of conversations.
No reporters were singled out as potential criminals, but the scope of the subpoena surrounding leak of classified information provoked outrage among media and concern from civil libertarians, privacy advocates and some members of Congress.
A second, similar case involving a Fox News reporter's e-mails regarding a separate leak of classified information on an unrelated national security story added fuel to the media controversy.
President Barack Obama has said he was "troubled by the possibility that leak investigations may chill the investigative journalism that holds government accountable."
Pruitt said the AP could have helped the Justice Department narrow the scope of the subpoena had it "come to us in advance."
He added that a court could have decided the matter if the DOJ and the AP didn't agree.
"There was never that opportunity. Instead, the DOJ acted as judge, jury and executioner in private -- in secret," he said.
The Justice Department defended its scrutiny, saying previously that it followed its own regulations in acquiring subpoenas and exhausted other methods to find out who might have leaked the information before seeking phone records.
It said investigators conducted more than 550 interviews and examined tens of thousands of pages of documents before issuing subpoenas involving phone lines.
Justice Department rules call for negotiations with news organizations on such issues unless there is a "substantial threat to the integrity of the investigation."
Attorney General Eric Holder has subsequently said he will never prosecute reporters for doing their job.
Pruitt, who is also a First Amendment lawyer, worries about precedent.
"If reporters' phone records are now open territory for the government to secretly monitor, then news sources will be intimidated from talking to reporters. The AP is not going to be intimidated, but our sources will be," Pruitt said.
Pruitt says other news organizations also have experienced sources worried about speaking to them.
"This chilling effect is not just at AP. ... Journalists from other news organizations have personally told me (the DOJ's seizing of AP's phone records) has intimidated sources from speaking to them," he said.
Holder has launched a review of Justice Department guidelines on investigations involving the press, and has met with media executives about it.
Obama has given Holder a July 12 deadline to come up with some suggestions for possibly changing the approach.