The letter, sent by AP President and Chief Executive Officer Gary Pruitt called the examination of 20 telephone lines an "unprecedented intrusion" into the news coop's newsgathering activities.
He said the AP's lawyers were informed by letter Friday the information was obtained earlier this year.
"The records that were secretly obtained cover a full two-month period in early 2012 and, at least as described in Mr. [U.S. Attorney Ronald C.] Machen's letter, include all such records for, among other phone lines, an AP general phone number in New York City as well as AP bureaus in New York City, Washington, D.C., Hartford, Connecticut, and at the House of Representatives," Pruitt said. "This action was taken without advance notice to AP or to any of the affected journalists, and even after the fact no notice has been sent to individual journalists whose home phones and cellphone records were seized by the Department.
"There can be no possible justification for such an overbroad collection of the telephone communications of The Associated Press and its reporters."
The Hill reported the investigation may have been related to a report involving a foiled 2012 terror plot in Yemen.
The U.S. attorney's office in Washington issued a statement saying it is 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."
Asked about an administration response, White House press secretary Jay Carney referred questions to the Justice Department.
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