The latest revelations about top secret information traversing Hillary Clinton's private email server have triggered accusations that someone in her "inner circle" likely stripped the classification markings, illegally. 

The claims come after the Clinton campaign stuck to the argument that the Democratic presidential candidate, while secretary of state, never dealt with emails that were "marked" classified at the time. 

"Hillary only used her personal account for unclassified email. No information in her emails was marked classified at the time she sent or received them," campaign Communications Director Jennifer Palmieri said in a statement to supporters Wednesday. 

But a State Department official told Fox News that the intelligence community inspector general, who raised the most recent concerns about Clinton's emails, made clear that at least one of those messages contained information that only could have come from the intelligence community. 

"If so, they would have had to come in with all the appropriate classification markings," the official said. 

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The official questioned whether someone, then, tampered with that message. "[S]omewhere between the point they came into the building and the time they reached HRC's server, someone would have had to strip the classification markings from that information before it was transmitted to HRC's personal email." 

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The official said doing so would "constitute a felony, in and of itself. I can't imagine that a rank-and-file career DOS employee would have done this, so it was most likely done by someone in her inner circle." 

The messages apparently contained satellite imagery and signals intelligence, information that diplomats cannot unilaterally obtain. 

Yet, like the Clinton campaign, the State Department public affairs team also maintains that the emails were "not marked classified" when Clinton received them. 

"None of them were classified at the time," department spokesman Mark Toner said. 

Asked Thursday whether there's any indication classification markings were taken off the documents, department spokesman John Kirby said they have no indications any markings were stripped. 

With Clinton's server and thumb drive now in the possession of the FBI, questions about whether classification markings were tampered with are just part of the puzzle -- and only one factor that is complicating Clinton's frontrunning bid for the Democratic presidential nomination. 

Fox News has confirmed that the server itself was picked up by the FBI on Wednesday in New Jersey, at a third-party data center. But someone from that cyber-management company told the Washington Post that the server they forked over is blank, because everything on it was transferred during a 2013 upgrade. 

As part of a separate but related lawsuit brought by the conservative group Judicial Watch, a letter was also filed Wednesday night from State Department Under Secretary for Management Patrick Kennedy forwarding a judicial order to lawyers for Clinton and top adviser Huma Abedin to not delete any federal records. The attorneys say they will comply. 

Clinton announced that she would turn the server over to the FBI Tuesday. That same day, Intelligence Community Inspector General I. Charles McCullough III told members of Congress that at least two emails that traversed the device while she was secretary of state contained information that warranted one of the government's highest levels of classification. 

The latest email revelations have thrown a major wrench into Clinton's 2016 presidential campaign, though Palmieri shrugged off the ongoing investigation in her email to supporters Wednesday. 

"Look, this kind of nonsense comes with the territory of running for president," Palmieri said. "We know it, Hillary knows it, and we expect it to continue from now until Election Day." 

Meanwhile, Fox News has learned that top U.S. intelligence officials are running out of patience with the State Department's reluctance to turn over emails from the server. 

The intelligence community's inspector general has requested approximately 30,000 emails from Clinton's tenure as secretary of state in order to conduct its own review. 

Those emails are in possession of the State Department, which has been gradually releasing them to the public. 

An intelligence source told Fox News the State Department has pushed back on the government intelligence watchdog's request, and that Director of National Intelligence James Clapper is considering intervening. The source said the inspector general wants to check the controls on the redaction process and ensure that the office can get a handle on all of the potentially sensitive information that was contained in the Clinton emails. 

Fox News' James Rosen, Peter Doocy, Mike Emanuel and Matthew Dean and The Associated Press contributed to this report.