Acrimony between the FBI and the Justice Department was so bad in the waning days of the Obama administration that some agents quit the bureau in frustration, a former G-man says.

Fractures which began during the tenure of former Attorney General Eric H. Holder Jr. deepened in the later years, and particularly in the run-up to the 2016 president election.

The depths of the antagonism were exposed in an inspector general’s report last week looking into former FBI Deputy Director Andrew McCabe, who was fired from the FBI earlier this year for misleading multiple investigations. While saying Mr. McCabe lacked candor in questioning, some of it under oath, the report went much deeper, describing the rift between the bureau and its political masters at the department.

Investigators details one instance in August when Mr. McCabe got a call from a senior Justice Department official who complained about the FBI’s “overt” actions probing the Clinton Foundation in the middle of the campaign.

Mr. McCabe said he got the sense the Obama-era Justice Department was telling him “to shut down” the probe. Later he called the exchange as “very dramatic” and said he’d never had a confrontation like that with the Justice Department.

The report describes the relationship between the two agencies as “being under great stress,” and said Mr. McCabe was caught in “an increasingly acrimonious fight for control between the Justice Department and FBI pursuing the Clinton foundation case.”

Former agents said the acrimony started before the election.

One said the relationship fractured under Mr. Holder as agents in field offices across the country did not trust Justice Department lawyers, whom they saw as Washington bureaucrats trying use investigations for political advantage.

The Justice Department, meanwhile, had become frustrated at the rank-and-file agents not always following orders and, at times, strongly disagreeing with superiors.

“I know from talking to some agents in the FBI at that time that there conflicts between the Holder DOJ and its priorities and how the FBI wanted to work cases,” said Danny Defenbaugh, a 33-year FBI agent who retired in 2002.

“The FBI had always taken pride in following the evidence to where it would lead and never allowing politics into their investigation decisions,” Mr. Defenbaugh continued. “But then the DOJ at times would say, ‘we don’t want you to do this.’”

One source of disagreement was Mr. Holder’s pressure on the FBI to investigate local police agencies for civil rights violations.

The department opened more than 20 civil rights investigations into local police departments between 2009 and 2014, more than doubling the number of reviews from the previous five years.

Some in law enforcement, including the FBI, were demoralized by the probes, believing they were risking their lives without any support from Main Justice in Washington, said a former Justice Department lawyer.

“Eric Holder waged an anti-police campaign that he believed in,” said J. Christian Adams, who served as an attorney in the Justice Department’s Civil Rights Division from 2005 through 2010. “He was so successful in merging his ideology with the Justice Department some people there didn’t even realize he was doing it.”

The battle intensified in 2014 as the Justice Department and the FBI field office that would later investigate former Secretary of State Hillary Clinton went to war over the death of Eric Garner in New York City. Mr. Garner died in July of that year after a New York City Police Officer confronted him for selling untaxed cigarettes. The officer was seen on video using a chokehold, prohibited by the New York Police Department, to subdue him.

FBI agents took over the case and opposed charging the officer, a recommendation supported by New York federal prosecutors. Attorneys at the Justice Department’s Civil Rights Division claimed there was clear evidence to the charge the officer.

Then-Attorney General Loretta E. Lynch removed the FBI agents investigating the case, replacing them with agents from outside New York. The move was described as “highly unusual.” Ultimately, a federal grand jury decided not to indict the officer, Daniel Pantaleo.

Stress from the Garner skirmish was still fresh at the FBI and Justice Department when the Clinton investigations began. It had FBI officials worried about how much Washington would interfere with their work.

“Holder and Lynch totally politicized the Justice Department,” said Hans von Spakovsky, a former Justice Department attorney who now works with The Heritage Foundation. “There was no compunction about interfering with a criminal investigation.”

But others say tensions are a result of cultural differences endemic to both organizations, with one side tending toward the hard-charging crime-stoppers and the other the more cautions legal wranglers.

One complication is that FBI agents typically deal with local U.S. Attorneys Offices, which are more aggressive and make decisions fairly quickly, said Ron Sievert, a former Justice Department attorney and current University of Texas professor.

Mr. Sievert estimates that those local prosecutors end up handling about 90 percent of FBI investigations, while officials at department headquarters in Washington chiefly get involved in political corruption, national security or interstate drug trafficking cases.

“For years, Main Justice had a reputation for being overly cautious,” Mr. Sievert said. “What you can do with one supervisor’s signature in the field you have to do with three or five in Washington because everyone is thinking about the political and legal ramifications of each case.”

Mr. Sievert recalled his own difficulty getting a program approved during his time at the Justice Department. It took about fourth months to secure support from each supervisor in the chain of command.

When his project was finally green-lit by the attorney general himself, Mr. Sievert was told that he now had to seek approval from the Treasury and Commerce departments along with the intelligence agencies — a process that would take about four more months for each department.

“At the U.S. Attorney’s Office, if you have a great idea that makes sense and legal, they will tell you to just go for it,” he said.

Mr. Adams said it could take years to repair the division, and it could require a housecleaning of leadership at both the FBI and Justice Department.

“The problem is so vast and deeply imbedded in the Justice Department, it will be an extremely difficult thing to dislodge,” Mr. Adams said.

Lew Schiliro, the former head of the FBI’s New York field office, said Attorney General Jeff Sessions needs to take the reins.

“It has to be Sessions,” he said. “The bureau reports to him and the Justice Department reports to him, yet he’s been silent on the issue. He needs to be a strong attorney general.”

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