The dispute centered on an ambiguous description in the original notice to The A.P., which an employee of the news organization said was sent as an attachment to an e-mail on May 10 from Jonathan M. Malis, a federal prosecutor, to several A.P. employees.

The attached letter, the employee said, consisted of a single sentence citing the Justice Department regulation for obtaining journalists’ telephone records, and saying that The A.P. “is hereby notified that the United States Department of Justice has received toll records from April and May 2012 in response to subpoenas issued” for 20 phone numbers in five area codes and three states.

The regulation requires subpoenas for reporters’ tolling records — logs of calls made and received — to be narrowly focused and undertaken only after other ways of obtaining information are exhausted. Under normal circumstances, news organizations are to be notified ahead of time so they can negotiate or ask a judge to quash the subpoena, but the regulation allows exceptions, in which case journalists must be notified no later than 90 days afterward.

Mr. Cole said the department had undertaken “a comprehensive investigation” before seeking the phone records, including more than 550 interviews and a review of “tens of thousands of documents.” The calling records, he added, “have been closely held and reviewed solely for the purposes of this ongoing criminal investigation” and would not be used in any other case.

The A.P. on Tuesday was still examining whether any telephone companies had tried to challenge the subpoena on its behalf before cooperating. But at least two of the journalists’ personal cellphone records were provided to the government by Verizon Wireless without any attempt to obtain permission to tell them so the reporters could ask a court to quash the subpoena, the employee said. Debra Lewis, a Verizon Wireless spokeswoman, said the company “complies with legal processes for requests for information by law enforcement,” but would not comment on any specific case.

Lucy Dalglish, dean of the journalism school at the University of Maryland, criticized the Justice Department’s broad seizure of phone records, saying it would chill the ability of reporters to report the news. The subpoena came against the backdrop of six prosecutions of officials in leak-related cases under President Obama — twice the number prosecuted under all previous presidents combined.