The plight of reporter James Rosen had further riled Washington journalists already angered by the department's seizure of phone records of the Associated Press in a different investigation into national security leaks.
While declining to comment on specific cases, White House spokesman Jay Carney said that Obama was deeply committed to freedom of the press, enshrined in the First Amendment to the US constitution.
"The president believes this deeply -- that the press is allowed to pursue investigative journalism freely. He is a fierce defender of the First Amendment, of press freedom, and will continue to be.
Carney, a former Time magazine reporter, was hammered over Rosen's case in his daily briefing yesterday, and said he had subsequently talked to his boss about the issue to further divine his thoughts.
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The Washington Post reported this week that Rosen's emails and phone records and even data from his State Department security badge were surveyed by US government investigators.
There were suggestions he could be named as an "unindicted co-conspirator" in a case against Stephen Jin-Woo Kim, a former State Department official accused of leaking him classified information on North Korea.
Prominent journalism organisations and press freedom advocates have warned that the Obama administration, which has taken a hard line against leakers, could be infringing cherished press freedoms with its actions.
Obama argued last week that there was a balance to be struck between press freedoms and the lives of covert US operatives overseas.
"Leaks related to national security can put people at risk," Obama said.
He said his administration is working on "finding a way to strike that balance appropriately.