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

The FBI’s demand that Apple help unlock an iPhone used by one of the San Bernardino killers has outraged Silicon Valley, a significant source of political support for President Obama and Democrats.

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Comey, meanwhile, has stirred tensions by linking rising violent crime rates to the Black Lives Matter movement’s focus on police violence and by warning about “gaps” in the screening process for Syrian refugees.

Then there’s the biggest issue of all: the FBI’s investigation into the private email server used by Hillary Clinton Hillary Diane Rodham ClintonHillicon Valley: FBI chief says Russia is trying to interfere in election to undermine Biden | Treasury Dept. sanctions Iranian government-backed hackers The Hill's Campaign Report: Arizona shifts towards Biden | Biden prepares for drive-in town hall | New Biden ad targets Latino voters FBI chief says Russia is trying to interfere in election to undermine Biden MORE, 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.

In these cases and more, Comey — a Republican who donated in 2012 to Mitt Romney — has proved he is “not attached to the strings of the White House,” said Ron Hosko, the former head of the FBI’s criminal investigative division and a critic of Obama’s law enforcement strategies.

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.

With regards to the Apple standoff, “It’s just not clear [Comey] is speaking for the administration,” said Richard Clarke, a former White House counterterrorism and cybersecurity chief. “We know there have been administration meetings on this for months. The proposal that Comey had made on encryption was rejected by the administration.”

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 biographer, with whom he had a personal relationship.

“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.”

Hosko suggested that a showdown over potential criminal charges for Clinton could lead to a reprise of the famous 2004 hospital scene, when Comey threatened to resign.

“He has that mantle,” Hosko said. “I think now there’s this expectation — I hope it’s a fair one — that he’ll do it again if he has to.”

Comey’s independent streak has also been on display in the Apple fight, when his bureau decided to seek a court order demanding that the tech giant create new software to bypass security tools on an iPhone used by Syed Rizwan Farook, one of the two terrorist attackers in San Bernardino, Calif.

Many observers questioned whether the FBI was making an end-run around the White House, which had previously dismissed a series of proposals that would force companies to decrypt data upon government request.

“I think there’s actually some people that don’t think with one mindset on this issue within the administration,” said Sen. Tom Carper Thomas (Tom) Richard CarperDemocrat asks for probe of EPA's use of politically appointed lawyers Overnight Energy: Study links coronavirus mortality to air pollution exposure | Low-income, minority households pay more for utilities: report OVERNIGHT ENERGY: Democrats push resolution to battle climate change, sluggish economy and racial injustice | Senators reach compromise on greenhouse gas amendment stalling energy bill | Trump courts Florida voters with offshore drilling moratorium MORE (D-Del.), the Senate Homeland Security Committee’s top Democrat, at a Tuesday hearing. “It’s a tough issue.”

While the White House has repeatedly backed the FBI’s decision, it has not fully endorsed the potential policy ramifications, leaving some to think a gap might develop as similar cases pop up. The White House is poised to soon issue its own policy paper on the subject of data encryption.

“The position taken by the FBI is at odds with the concerns expressed by individuals [in the White House] who were looking into the encryption issue,” said Neema Singh Guliani, a legislative counsel with the American Civil Liberties Union (ACLU).

This week, White House homeland security adviser Lisa Monaco tried to downplay the differences between the two sides. The White House and FBI are both grappling with the same problems, she said in a discussion at the Council on Foreign Relations.

“There is a recognition across the administration that the virtues of strong encryption are without a doubt,” Monaco said on Monday. “There is also uniformity about the recognition that strong encryption poses real challenges.”

But former officials see Comey as wanting to blaze his own trail on the topic.

“I have been very surprised at how public and inflammatory, frankly, the FBI and the Justice Department’s approach has been on this,” said Chris Finan, a former National Security Council cybersecurity adviser.

“That doesn’t tend to be the administration’s preferred approach to handling things.”