The wording was contained in a redacted search warrant and other court papers that were previously under seal in the investigation of an online relationship between Weiner, the estranged husband of top Clinton aide Huma Abedin, and a teenage girl in North Carolina.
The papers offered no new revelations about Clinton's emails or the scope of a case that factored into the presidential election.
The classification "is significant because it means that the unauthorized disclosure of those emails could result in exceptionally grave damage to national security," the agent wrote.
In the Weiner probe, the FBI discovered header information on emails pointing to correspondence to and from Clinton, the papers say. Given the findings of the earlier probe, "there is also probable cause to believe that the correspondence ... Contains classified information which was produced by and is owned by the U.S. Government," they say.
The judge also ordered the redaction of sections of the paperwork related to the ongoing investigation into Weiner's online correspondence.
The discovery of the emails on the disgraced New York congressman's laptop prompted FBI Director James Comey to briefly reopen an investigation that he had closed over the summer into Clinton's use of the private server to handle emails she sent and received as secretary of state.
In statement, E Randol Schoenberg, a Los Angeles lawyer who had sued to obtain the court papers, said today that he saw "nothing at all in the search warrant application that would give rise to probable cause, nothing that would make anyone suspect that there was anything on the laptop beyond what the FBI had already searched and determined not to be evidence of a crime, nothing to suggest that there would be anything other than routine correspondence between Secretary Clinton and her longtime aide Huma Abedin.
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