In mid-July, President Trump gave a prime-time speech in which he raised concerns about a disputed F.B.I. report that China had tried to interfere in the 2020 election in an effort to defeat him.

At the heart of his address was a bitter complaint: that some of the bureau’s intelligence officials had purposefully sought to play down the report to undercut his claims about the race.

One day after Mr. Trump attacked those officials on TV, calling for their prosecution, Kash Patel, the F.B.I. director, sent a letter to the U.S. attorney’s office in Kansas City ordering that some of them immediately be investigated for obstruction and conspiracy, one of the agents assigned to the case testified on Tuesday.

The agent, Bryan Witt, said that even though the inquiry was generally viewed inside his office as a “witch hunt” and that he himself had concerns it was “political,” it nonetheless moved forward. And last week, one of the intelligence officials whom Mr. Trump had complained about was charged along with a colleague with lying to Congress about the roles they had played in another one of the president’s longstanding obsessions: the investigations into Hunter Biden, the former president’s son.

Mr. Witt’s explosive testimony, offered at a hearing in Federal District Court in Washington, was the latest account of just how tight a grip the White House has on decision-making at the F.B.I. and just how willing Mr. Patel has been to take orders from the president to go after people he believes to be enemies.

A veteran agent, Mr. Witt asserted from the stand that he had never before worked on a case where instructions came directly from the F.B.I.’s director. He added that Mr. Patel and his deputies often checked on his progress, pressing him and his colleagues to move as aggressively as possible.

The daylong hearing was nominally held so that lawyers for the two defendants — Nikki Floris and Bradley Benavides — could question the basis of the criminal complaint that was filed on Friday. It accused them of lying to the House Judiciary Committee in 2023 when they were questioned about the roles they had played in the F.B.I.’s investigations into Mr. Biden and his ties to foreign nationals and companies.

But as the day went on, the proceeding gradually turned into something more substantial as the lawyers got Mr. Witt to expose the ways in which Mr. Trump had directed Mr. Patel to use the power of the F.B.I. to investigate people he believed had cast doubts on both his lies about the 2020 election and his unsubstantiated claims that his opponent in that race, Joseph R. Biden Jr., had engaged in corrupt dealings in Ukraine while Hunter Biden had been working there.

Mr. Witt testified that he was originally instructed by Mr. Patel to investigate Ms. Floris and other F.B.I. intelligence officials after they had questioned a report from an informant developed by the bureau’s Albany field office that China had sought to tip the 2020 election in Mr. Biden’s favor.

But after he and his colleagues were unable to find evidence to support the claims, he said the inquiry quickly pivoted toward the testimony that Ms. Floris and Mr. Benavides had given three years ago in front of the House committee, which had been looking into Hunter Biden’s business dealings overseas.

Both Ms. Floris and Mr. Benavides served on the F.B.I.’s Foreign Influence Task Force, a group created after Russia interfered in the 2016 election. It helped intelligence agencies monitor clandestine efforts by foreign governments to manipulate American politics, including by issuing warnings about covert foreign meddling to politicians and social media companies.

Members of the task force had relayed warnings from the intelligence community about a covert Russian disinformation operation aimed at helping Mr. Trump win re-election in 2020 by amplifying claims that the elder Mr. Biden had engaged in corrupt dealings in Ukraine, where his son held a board seat on an energy firm, Burisma.

The case against Ms. Floris and Mr. Benavides is largely based on discrepancies between what they told Congress about their participation in the Biden investigations, what witnesses have said and what documents emerging from the inquiries have shown. Their lawyers spent much of Tuesday trying to persuade the magistrate judge handling the case, Zia M. Faruqui, that their clients had not lied to Congress and that the statements they had made had not materially affected the work of the House committee.

From the start, the prosecution has been marked by a series of unusual procedural maneuvers — including the fact that Ms. Floris and Mr. Benavides were charged in a criminal complaint, not an indictment. Complaints are typically used when prosecutors need to act quickly or have fears that defendants might flee. But Judge Faruqui said in court on Tuesday that both of the defendants are well-respected former agents and that the underlying facts of the case are more than three years old.

Judge Faruqui also expressed concern about another unorthodox tactic the Justice Department has used in the case. Late Monday night, prosecutors filed an amended complaint, adding a new charge of obstruction of Congress. But in an extraordinary break from standard legal practice, the prosecutors issued the new complaint without first seeking judicial approval, effectively asserting that they could accuse the defendants of additional crimes without the traditional checks and balances.

One of the prosecutors on the case, John Borchert, acknowledged it was a “novel” move to seek a criminal charge with first getting the approval of a jurist or grand jury. But Judge Faruqui said it was far more serious than that.

“It’s not just novel, Mr. Borchert,” he said. “It’s never been done before.”

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