Updated Monday 5/27 3:00 a.m. ET
(CNN)– The parent company of Fox News was aware years ago that the Justice Department was targeting one of its reporters in a leak investigation, sources said.
One law enforcement source said the Justice Department notified a media organization three years ago of a subpoena for detailed telephone records, and a second told CNN that organization was Fox News.
After that news broke, a Fox News executive said the Justice Department notified Fox's parent company News Corporation of the subpoena in May 2010. But Fox News itself apparently never got the word.
The subpoena came as the Justice Department was investigating Stephen Kim, a former State Department worker accused of the unauthorized disclosure of sensitive information to James Rosen, a Fox News reporter.
It is standard procedure for Justice Department officials to notify news organizations when they subpoena an outlet or its reporters.
CNN and other media outlets have previously reported a separate Justice Department query into Rosen's e-mails. With the approval of Attorney General Eric Holder, Justice officials obtained a warrant from a federal judge to access Rosen's e-mails.
While Fox News is now acknowledging that the Justice Department notified its parent company about the phone records search, that notice apparently did not include anything about the separate search of Rosen's e-mail.
"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," a law enforcement source told CNN. "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."
News Corporation spokesman Nathaniel Brown responded Sunday night in a carefully worded statement.
“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,” Brown said. “We are looking into this matter.”
In a New York Times article, Lawrence A. Jacobs, a former chief legal officer for News Corporation, said he never saw a notification about the phone records. He left the post in June 2011.
“I would have remembered getting a fax from the Justice Department,” Jacobs told the Times in an interview on Sunday. “These are not the kinds of things that happen every day.”
Fox has said it learned of the warrant for e-mails only recently, and newly released court documents show the government was trying to keep the investigation under seal. The network did not disclose to its viewers that the phone records had been subpoenaed.
The government's notice did not detail the extent of the investigation, in which the government labeled Rosen a possible co-conspirator. An FBI affidavit used to obtain the warrant for Rosen's e-mails described him as potentially being an "aider and abettor and/or co-conspirator" to the crime of disclosing government secrets.
The Justice Department has come under scrutiny this month as news broke of two government probes into reporters' records. Besides the Rosen case, the Associated Press announced the department had dug into the phone records of its reporters, including work, cell, and home lines.
–CNN's Julie Cannold contributed to this report