At a Senate hearing in March, Senator Charles E. Grassley, Republican of Iowa, spent seven minutes grilling Attorney General Merrick B. Garland about the Hunter Biden investigation, reading a series of unusually specific queries from a paper in his hands.

Did David C. Weiss, the Trump-appointed U.S. attorney in Delaware kept on under Mr. Garland to continue overseeing the inquiry, have full authority to bring charges against President Biden’s son in California and Washington if he wanted to? Had Mr. Weiss ever asked to be made a special counsel? Was the investigation truly insulated from political considerations?

That encounter has taken on new significance after House Republicans released testimony last week from a senior Internal Revenue Service investigator on the case that appeared to contradict Mr. Garland’s assurances to Mr. Grassley and others that Mr. Weiss had all the freedom and authority he needed to pursue the case as he saw fit.

The I.R.S. official, Gary Shapley, oversaw the agency’s role in the investigation of Mr. Biden’s taxes and says his criticism of the Justice Department led to him being denied a promotion. He told the House Ways and Means Committee that Mr. Weiss had been rebuffed by top federal prosecutors in Los Angeles and Washington when he had raised the prospect of pursuing charges against the president’s son in those jurisdictions.

Mr. Shapley, testifying under what Republicans say are whistle-blower protections, also said that he had witnessed Mr. Weiss saying last year that he would not be the “deciding official” regarding whether to prosecute Mr. Biden, and that Mr. Weiss had been turned down when he sought special counsel status, which would have allowed him greater flexibility in handling the case.

In providing accounts of internal discussions at odds with Mr. Garland’s testimony, Mr. Shapley gave Republicans a fresh opening to raise questions about the case and to cast doubt on the Justice Department’s repeated statements that Mr. Weiss had complete control of the investigation with no political interference.

But it remains unclear how much of the difference in the accounts reflects possible factors like miscommunication, clashing substantive judgments among agencies over how best to pursue a prosecution, or personal enmity among officials working on a high-pressure, high-profile case. Investigators like Mr. Shapley whose job it is to uncover evidence often have different perspectives from prosecutors who have to take into account how to treat defendants fairly and present cases to juries.

Republican efforts to link Hunter Biden’s problems to his father have often come up short, and Mr. Garland, a former federal appeals court judge, has taken pains to distance himself from core decision-making in the politically polarizing cases that have landed on his desk. Still, Republican leaders now see Mr. Garland as a potentially vulnerable figure as they look for ways to undercut the president heading into the 2024 campaign.

“If it comes true what the I.R.S. whistle-blower is saying, we’re going to start impeachment inquiries on the attorney general,” Speaker Kevin McCarthy told Fox News on Monday.

Mr. Garland, addressing reporters on Friday, forcefully denied Mr. Shapley’s claims. Mr. Weiss said in a letter to Congress this month that he had not been constrained in pursuing the investigation. Mr. Weiss said in the letter, dated June 7, that he had been “granted ultimate authority over this matter, including responsibility for deciding where, when and whether to file charges.” He has yet to face more specific questions from House Republicans in the wake of Mr. Shapley’s testimony.

White House officials dismissed Mr. McCarthy’s impeachment threat as a “distraction.” And Hunter Biden’s lawyers have told the Justice Department that Mr. Shapley has broken federal laws that keep grand jury material secret. Mr. Shapley’s lawyer, Mark D. Lytle, said his client “has legally protected rights to blow the whistle.”

“There are so many unanswered questions here that I think the only solution is having Garland or Weiss, or both, testify before Congress or have a long press conference where they answer everything that’s being thrown at them,” said John P. Fishwick Jr., who served as U.S. attorney for the Western District of Virginia from 2015 to 2017.

“Is this just a disgruntled guy who didn’t get his way, as happens in every investigation?” he added, referring to Mr. Shapley. “Or is there something else going on?”

Mr. Weiss announced this month that Mr. Biden had agreed to plead guilty to two misdemeanor charges of having failed to file his 2017 and 2018 taxes on time. Mr. Weiss also charged Mr. Biden in connection with his purchase of a handgun in 2018 but said he would not prosecute the charge under a two-year pretrial diversion program.

The Hunter Biden investigation was initiated by the Trump Justice Department in 2018 and eventually handed to Mr. Weiss, a Republican whose reputation for nonpartisanship had earned him the support of Delaware’s two Democratic senators during his confirmation a few months earlier.

Mr. Weiss was, according to the committee’s transcripts, determined to keep the inquiry under wraps as long as possible, thanking his team for keeping the investigation secret in a strategy session shortly after the 2020 election.

After President Biden was elected, the department’s interim leadership kept Mr. Weiss in place and in charge of the inquiry. Mr. Garland, after being confirmed, continued that arrangement, and was eager to avoid any suggestion of political meddling, according to people in his orbit.

But if Mr. Garland was content with how the politically explosive case was being handled, Mr. Shapley, a 14-year I.R.S. employee, was stewing in the shadows.

He recounted in his testimony that he had been arguing in meetings with Mr. Weiss and other prosecutors to aggressively pursue charges against Mr. Biden stemming from his failure to pay taxes in 2014 and 2015, two years not covered under Mr. Biden’s agreement to plead guilty on the misdemeanor tax charges. During those years, Mr. Biden was earning income from work for a Ukraine-based energy company and Chinese clients that Mr. Shapley suggested was being channeled through entities that had a presence in Washington and the Los Angeles area.

It is not clear if Mr. Weiss was convinced those strands of the investigation should be prosecuted or was simply making sure all potential charges were pursued thoroughly. But in mid-2022, Mr. Weiss reached out to the top federal prosecutor in Washington, Matthew Graves, to ask his office to pursue charges and was rebuffed, according to Mr. Shapley’s testimony.

A similar request to prosecutors in the Central District of California, which includes Los Angeles, was also rejected, Mr. Shapley testified. A second former I.R.S. official, who has not been identified, told House Republicans the same story. That episode was confirmed independently to The New York Times by a person with knowledge of the situation.

While Mr. Weiss had the authority to pursue leads that led to jurisdictions other than his own in Delaware, the department’s practices dictated that he secure the approval and cooperation of the U.S. attorneys in those districts before proceeding.

If Mr. Weiss wanted to move ahead without their approval, he could have brought the issue to Mr. Garland’s attention, and the attorney general could then appoint him “special attorney,” which would allow him to bypass the standard chain of command. There is no indication that Mr. Weiss appealed for help from Mr. Garland or his top deputies — or that he even communicated about the case with anyone in leadership beyond the department’s top career official at headquarters.

When Mr. Grassley, at the hearing in March, pressed Mr. Garland on that point — without referring explicitly to Mr. Shapley’s claim, which would not become public for months, but tracking closely what Mr. Shapley would tell the Ways and Means Committee — the attorney general said he would “assure” that Mr. Weiss would be able to bring charges outside Delaware if that was his wish. At a news conference after the transcript was released, Mr. Garland repeated that message.

As the investigation ground on, Mr. Shapley had grown disenchanted with the lack of progress in the investigation, and by his account was so upset over the conduct of the Justice Department he found it hard to sleep.

He testified that Mr. Weiss, despite his public statements to the contrary, was also unhappy, and that he complained about being handcuffed by higher-ups in the department.

Things came to a head during a meeting among investigators on Oct. 7, when Mr. Weiss made an unexpected admission to him in the presence of several other federal law enforcement officials, according to Mr. Shapley’s account.

“He surprised us by telling us on the charges, quote: ‘I’m not the deciding official on whether charges are filed,’” said Mr. Shapley, a longtime Republican who has said he is motivated by the evenhanded application of justice, not politics.

“To add to the surprise, U.S. Attorney Weiss stated that he subsequently asked for special counsel authority from Main D.O.J. at that time and was denied that authority,” he added.

Mr. Weiss, he said, was then told “to follow D.O.J.’s process.”

Mr. Shapley did not say if Mr. Weiss told him who had turned down his request to appoint a special counsel, a decision that can only be made by an attorney general under department regulations.

After Mr. Garland last week denied Mr. Shapley’s account, Mr. Shapley’s lawyer, Mr. Lytle, issued a statement naming six F.B.I. and I.R.S. agents who he said witnessed the exchange, which Mr. Shapley also recorded in a contemporaneous email.

Later, Mr. Shapley blamed Mr. Weiss, without evidence, for helping to kill a promotion he had hoped to get, by criticizing him to his superiors at the I.R.S.

“I think it tainted me,” he told the Ways and Means Committee. “I think that they retaliated against me because of that. There’s really no other explanation for it.”

A spokeswoman for Mr. Weiss did not return a request for comment. In his June 7 letter to Representative Jim Jordan, chairman of the House Judiciary Committee, he wrote that he had “ultimate authority” over every aspect of the investigation, which seemed to contradict Mr. Shapley’s claim that he had said he was not the deciding official in the case. (On Monday, Mr. Jordan sent a letter asking Mr. Weiss to clarify what “ultimate authority” means.)

In a short news release last week setting out the terms of the deal with Mr. Biden, Mr. Weiss added without explanation: “The investigation is ongoing.” It is unclear whether that phrase was just Justice Department boilerplate, a hint about the possibility of more charges arising from the inquiry or a shield against demands for documents and testimony about the Biden case from Congress.

Mr. Garland, who often sidesteps requests for comment on ongoing investigations, has been uncharacteristically blunt in refuting Mr. Shapley’s testimony.

“Mr. Weiss never made that request,” Mr. Garland told reporters last Friday, referring to whether Mr. Weiss had sought special counsel status.

Under the special counsel regulation, Mr. Weiss would have been required to inform Mr. Garland about any major developments in the investigation, including his request to bring charges in California and Washington. Mr. Garland, in turn, would have to inform Congress in writing if he decided to overrule any major investigative decision, like charging Mr. Biden.

“If you provided the Delaware U.S. attorney with special counsel authority, isn’t it true that he would not need permission from another U.S. attorney to bring charges?” asked Mr. Grassley, a longtime chairman of the Senate Judiciary Committee, in March.

“It’s a kind of a complicated question,” replied Mr. Garland.

He then suggested it was also an irrelevant one, arguing that Mr. Weiss “already” possessed the same authority under both scenarios.

Mr. Grassley did not appear to be convinced.

Adam Goldman and Luke Broadwater contributed reporting.

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