The media conglomerate was responding to the US Justice Department, which said it told News Corp about the seizure of phone records for James Rosen, a reporter with Fox News, in August 2010.
"While we don't take issue with the DoJ's account that they sent a notice to News Corp, we do not have a record of ever having received it," said News Corp spokesman Nathaniel Brown on Monday. He added the company is looking into the matter.
Fox News, which is owned by News Corp, has said it never received a notification from the government.
Lawrence Jacobs, the former worldwide general counsel at News Corp during 2010, told Reuters he had no recollection of ever receiving it nor had News Corp found any evidence when it combed through Jacobs' emails.
"I have no memory of it," he said.
A law enforcement official who asked not to be named said in a statement Monday that "In the investigation that led to the indictment of Stephen Kim, the government issued subpoenas for toll records for five phone numbers associated with the media. Consistent with Department of Justice policies and procedures, the government provided notification of those subpoenas nearly three years ago by certified mail, facsimile, and e-mail."
The official said notice went to both News Corp and to the reporter, Rosen.
The Fox subpoena is the latest twist involving an acrimonious battle between the media's right to publish and the government's ability to investigate leaks involving classified information.
Guidelines for the Justice Department have for decades required the personal involvement of the attorney general when prosecutors are considering a subpoena to the media and for the media organisation be notified of any action.
Last week, the Justice Department said that Attorney General Eric Holder and other senior officials vetted a decision to search an email account belonging to Rosen whose story on North Korea prompted a leak investigation.
Rosen reported in June 2009 that US intelligence officials believed North Korea would conduct more nuclear tests in response to UN sanctions.
Rosen's alleged source, former State Department analyst Stephen Kim, is scheduled to go to trial as soon as next year on charges that he violated an anti-espionage law. Rosen was not charged and prosecutors have given no indication they plan to charge him.
In a statement on Friday, the department said the May 2010 search warrant for the reporter's Google email account followed all laws and policies.
The Associated Press revealed earlier in May the government secretly seized the phone records of several AP offices and reporters describing the action as a "massive and unprecedented intrusion".
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