When the Justice Department began investigating possible leaks of classified information about North Korea in 2009, investigators did more than obtain telephone records of a working journalist suspected of receiving the secret material.

They used security badge access records to track the reporter’s comings and goings from the State Department, according to a newly obtained court affidavit. They traced the timing of his calls with a State Department security adviser suspected of sharing the classified report. They obtained a search warrant for the reporter’s personal e-mails.

The case of Stephen Jin-Woo Kim, the government adviser, and James Rosen, the chief Washington correspondent for Fox News, bears striking similarities to a sweeping leaks investigation disclosed last week in which federal investigators obtained records over two months of more than 20 telephone lines assigned to the Associated Press.

At a time when President Obama’s administration is under renewed scrutiny for an unprecedented number of leak investigations, the Kim case provides a rare glimpse into the inner workings of one such probe.

Court documents in the Kim case reveal how deeply investigators explored the private communications of a working journalist — and raise the question of how often journalists have been investigated as closely as Rosen was in 2010. The case also raises new concerns among critics of government secrecy about the possible stifling effect of these investigations on a critical element of press freedom: the exchange of information between reporters and their sources.

“Search warrants like these have a severe chilling effect on the free flow of important information to the public,” said First Amendment lawyer Charles Tobin, who has represented the Associated Press, but not in the current case. “That’s a very dangerous road to go down.”

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