FBI chief James Comey and his investigators are increasingly certain that presidential nominee Hillary Clinton violated laws in handling classified government information through her private email server, career agents say.

Some expect him to push for charges, but he faces a formidable obstacle: the political types in the Obama White House who view a Clinton presidency as a third Obama term.

With that, agents have been spreading the word, largely through associates in the private sector, that their boss is getting stonewalled, despite uncovering compelling evidence that Clinton broke the law.

Exactly what that evidence is — and how and when it was uncovered during Comey’s months-long inquiry — has not been disclosed. For the record, the FBI had no comment on the matter, and government sources say no final decision has been made.

Clinton denies she did anything wrong, claiming she had no idea she was getting classified information (a violation of federal law) on her private server during her years as Obama’s secretary of state because the documents she received contained no such headings.

And as FBI director, Comey can only recommend charges to the hacks in the Obama Justice Department. Indeed, many law enforcement officials who know the FBI chief and the bureau’s inner workings believe the evidence would have to be overwhelming for Comey to even recommend charges, much less for DOJ to pursue them.

Still, some FBI staffers suggest the probe’s at a point where Comey might quit in protest if Justice ignores a recommendation to pursue a criminal case against Clinton.

Just how close Comey is to any recommendation — whether to indict or exonerate Clinton — is difficult to know. But agents believe the probe is nearing an end. A State Department staffer who set up Clinton’s email server, for instance, was recently granted immunity from prosecution to provide Comey’s team with evidence.

“You don’t start granting people close to Clinton immunity unless you are seriously looking at charges against your target,” one former official told me.

I’m also told Comey and his team increasingly doubt Clinton’s story. Most officials know private email servers are easier to hack into than secure government servers. They also know that even documents not labeled “classified” may be top secret.

That’s why they’re supposed to be sent only through government accounts. Those who don’t follow those rules, like former CIA Director David Petraeus, have faced consequences.

Another matter for Comey & Co.: whether Clinton comingled her official State Department business with her role at the Clinton Foundation, and whether she wiped clean messages that show her using her office at State for foundation work.

Law enforcement sources also say Comey’s record as a prosecutor shows he has zero tolerance for such abuses.

As US attorney for the Southern District after the Nasdaq stock market crashed, Comey led an obstruction investigation that targeted Internet banker Frank Quattrone. That probe focused on a single (and some would say non-dispositive) sentence from a single email he appeared to approve, “Let’s clean up those files.”

Quattrone was convicted and faced several years in jail, though a successful appeal and deferred prosecution agreement with the government put the matter to rest.

Comey’s prosecution of domestic diva Martha Stewart followed a similar pattern. Stewart sold shares of a company owned by one of her friends just before a corporate announcement sent the stock into a tailspin.

But she did not go to jail for what the feds began investigating: insider trading. Instead, Comey & Co. had to settle on obstruction-of-justice charges based on allegedly misleading information Stewart gave about her trade. Even this was no slam dunk: At trial, witnesses contradicted each other. At least one of the charges in the case was dropped. (One prosecution witness later faced perjury charges over his testimony but was eventually acquitted.)

Yet in the end, Comey prevailed. Stewart was convicted and sentenced to several months in prison.

Yes, there are key differences with these cases, the biggest being political: Comey had the backing of his boss, then-President George W. Bush, to address alleged Wall Street improprieties.

FBI sources say he has no backing from President Obama and Attorney General Loretta Lynch to recommend charges against the former secretary, since a Clinton presidency may be the best chance to preserve the Obama legacy.

That leaves Comey in a bind: Does he do what is politically expedient and deny the reality that Clinton’s email server activities violated the law, or follow the evidence to wherever it takes him?

Here’s hoping he uses the same standards against Clinton as he used against Stewart and Quattrone.

Charles Gasparino is a Fox Business senior correspondent.