The affidavit, a request for e-mails from the Federal Bureau of Investigation, provided minute-by-minute details about what time both men came and left the State Department and the length of their phone conversations down to the second and also took the unusual step of labeling the reporter a potential “co-conspirator” in the leak of classified information about North Korea’s nuclear program.

In a memo to his staff this week, Roger Ailes, the chief executive of Fox News, said, “We reject the government’s efforts to criminalize the pursuit of investigative journalism and falsely characterize a Fox News reporter to a federal judge as a ‘co-conspirator’ in a crime,” and that “we will not allow a climate of press intimidation, unseen since the McCarthy era, to frighten any of us away from the truth.”

Josh Meyer, director of education and outreach at the Medill National Security Journalism Initiative at Northwestern University and a writer for Quartz, said that in the 30 years he has lived on and off in Washington, he has never found journalists to be so skittish about being under the government’s watchful eye.

“It’s so bad that there’s a gallows humor that has sort of emerged out of this,” Mr. Meyer said. “You see journalists at parties, and you joke about ‘How is the investigation going?’ ” People just assume they’re being investigated, and it’s not a good feeling.”

He said that he was “highly skeptical” of President Obama’s announcement. “One would think he would have done that months or years ago when these investigations were authorized.

In his speech, President Obama said that as part of its review the Justice Department would “convene a group of media organizations to hear their concerns.” Bruce D. Brown, the executive director of the Reporters Committee for Freedom of the Press, called the announcement “a welcome development,” but he remained cautious about what might actually result from these talks.

“We would want to come out of any such dialogue with an acknowledgment from the government that a reporter does not commit a crime when asking for information,” he said. “The second objective would be that the government honor its duties to notify the news media when it seeks journalists’ records. That will give the news media the proper opportunity to challenge those requests in court.”