The aggressive posture of the FBI under Director James Comey is becoming a political problem for the White House.

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Then there’s the biggest issue of all: the FBI’s investigation into the private email server used by Hillary Clinton, Obama’s former secretary of State and the leading contender to win the Democratic presidential nomination.

A decision by the FBI to charge Clinton or her top aides for mishandling classified information would be a shock to the political system.

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Publicly, administration officials have not betrayed any worry about the Clinton probe. They have also downplayed any differences of opinion on Apple.

But former officials say the FBI’s moves are clearly ruffling feathers within the administration.

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Comey has a reputation for speaking truth to power, dating back to a dramatic confrontation in 2004 when he rushed to a hospital to stop the Bush White House from renewing a warrantless wiretapping program while Attorney General John Ashcroft was gravely ill. Comey was Ashcroft’s deputy at the time.

That showdown won Comey plaudits from both sides of the aisle and made him an attractive pick to lead the FBI. But now that he’s in charge of the agency, the president might be getting more than he bargained for.

“Part of his role is to not necessarily be in lock step with the White House,” said Mitch Silber, a former intelligence official with the New York City Police Department and current senior managing director at FTI Consulting.

“He takes very seriously the fact that he works for the executive branch,” added Leo Taddeo, a former agent in the FBI’s cyber division. “But he also understands the importance of maintaining his independence as a law enforcement agency that needs to give not just the appearance of independence but the reality of it.”

The split over Clinton’s email server is the most politically charged issue facing the FBI, with nothing less than the race for the White House potentially at stake.

Obama has publicly defended Clinton, saying that while she “made a mistake” with her email setup, it was “not a situation in which America’s national security was endangered.”

But the FBI director has bristled at that statement, saying the president would not have any knowledge of the investigation. Comey, meanwhile, told lawmakers last week that he is “very close, personally,” to the probe.

Obama’s comments reflected a pattern, several former agents said, of the president making improper comments about FBI investigations. In 2012, he made similarly dismissive comments about a pending inquiry into then-CIA Director David Petraeus, who later pleaded guilty to a misdemeanor charge for giving classified information to his mistress and biographer, Paula Broadwell.

“It serves no one in the United States for the president to comment on ongoing investigations,” Taddeo said. “I just don’t see a purpose.”