WASHINGTON — A federal judge dismissed the criminal case against President Trump’s former national security adviser Michael T. Flynn on Tuesday, two weeks after Mr. Trump pardoned him, but portrayed the Justice Department’s previous arguments for dismissing the matter as “dubious to say the least” and suggested he “likely” would have rejected them.

In a 43-page opinion, Judge Emmet G. Sullivan of the Federal District Court for the District of Columbia expressed strong doubts about the legitimacy of Attorney General William P. Barr’s decision to try to end the case against Mr. Flynn even though he had twice pleaded guilty to lying to the F.B.I. But the judge said the subsequent pardon had rendered the legal question moot.

“The history of the Constitution, its structure, and the Supreme Court’s interpretation of the pardon power make clear that President Trump’s decision to pardon Mr. Flynn is a political decision, not a legal one,” Judge Sullivan wrote. “Because the law recognizes the president’s political power to pardon, the appropriate course is to dismiss this case as moot.”

The move appeared to bring to a close the twisting legal and political saga of Mr. Flynn, a decorated lieutenant general who was an early supporter of Mr. Trump’s 2016 campaign and got caught up in the beginning stages of the Russia investigation, resulting in his ouster days into the administration in 2017 and federal charges for making false statements to investigators.

Mr. Flynn — the only White House official charged in the Russia investigation by the special counsel, Robert S. Mueller III — lied to his colleagues and then the F.B.I. about conversations he had in December 2016 with the Russian ambassador to the United States, Sergey I. Kislyak. Mr. Flynn urged Moscow not to escalate in response to sanctions imposed by the departing Obama administration over Russia’s covert election interference to help Mr. Trump, and raised the possibility that the incoming Trump administration would work more closely with Russia.

Despite initially distancing himself from Mr. Flynn and dismissing him from his White House position, Mr. Trump later came to embrace the case as part of his campaign to attack the Russia investigation as a “deep state” conspiracy against him. Mr. Flynn eventually fired his legal team and hired a new defense lawyer, Sidney Powell, and sought to withdraw his guilty plea — saying he simply had not remembered the calls, which were intercepted.

But Judge Sullivan expressed skepticism.

“With regard to Mr. Flynn’s alleged ‘faulty memory,’ Mr. Flynn is not just anyone; he was the national security adviser to the president, clearly in a position of trust, who claimed that he forgot, within less than a month, that he personally asked for a favor from the Russian ambassador that undermined the policy of the sitting president prior to the president-elect taking office,” the judge wrote.

Last spring, after Mr. Flynn moved to withdraw his guilty plea, Mr. Barr directed the Justice Department to withdraw the charge against him. But Judge Sullivan held up the request to scrutinize its legitimacy, leading to a fight in an appeals court and then Mr. Trump’s pardon.

Judge Sullivan had appointed a retired federal judge and former mafia prosecutor, John Gleeson, to critique the department’s new stance. Mr. Gleeson argued that prosecutors’ rationale made no sense and could only be a pretext for a politically motivated favor to a presidential favorite. He urged Judge Sullivan to instead proceed to sentencing Mr. Flynn — an extraordinary prospect that, the judge wrote on Tuesday, had presented a “close question.”

Kerri Kupec, a spokeswoman for Mr. Barr, said in a statement, “Dismissal is, of course, the correct result.” Asked to comment on Judge Sullivan’s scathing dissection of the department’s arguments to dismiss the case before the pardon, she said her comment applied to the case both pre- and post-pardon. Mr. Trump, in a statement posted on Twitter, wrote: “Thank you and congratulations to General Flynn. He and his incredible family have suffered greatly!”

Before the pardon, the Justice Department’s main argument for dismissing the case despite Mr. Flynn’s guilty plea was that his lies to the F.B.I. were not a crime because they were not “material” to any legitimate investigation since the bureau had been moving to close an inquiry into whether Mr. Flynn was a Russian agent before his pattern of lying to colleagues about the Russian ambassador raised new suspicions.

That rationale was widely disputed, in part because F.B.I. agents have broad authority to conduct voluntary interviews and Mr. Flynn’s statements seemed obviously relevant to the larger investigation into the nature of any relationship between the Russian government and the Trump campaign.

In his opinion, Judge Sullivan said the department’s narrow definition of what counted as “material” in the Flynn matter was simply “not the law.” He called the government’s arguments “perplexing,” contrary to what it had previously said even in the Flynn case and unsupported by what prosecutors have said in any other false-statements case.

He wrote that to dismiss the case before the pardon, he would have had to be satisfied that the government undertook a “considered judgment,” but said prosecutors “likely” fell short.

The other major argument put forward by Mr. Barr’s prosecutors after the about-face was that the Justice Department was no longer certain it could prove beyond a reasonable doubt that Mr. Flynn uttered false statements, citing issues surrounding the F.B.I. interview that Mr. Flynn’s defenders have pointed to with suspicion.

Judge Sullivan rejected those arguments, too.

For example, Mr. Trump’s allies have emphasized that agents who interviewed him said that they did not detect signs that he was lying. But the judge said that was “irrelevant in a false-statements case.”

Mr. Trump’s allies have also argued that the F.B.I. set up Mr. Flynn, seizing on notes before a brainstorming session about how to question him that were written by William Priestap, the F.B.I.’s counterintelligence chief at the time. Mr. Priestap wrote: “What’s our goal? Truth/admission or to get him to lie, so we can prosecute him or get him fired?” But the judge wrote that “an objective interpretation of the notes in their entirety does not call into question the legitimacy of the interview.”

Moreover, he noted, prosecutors could have used Mr. Flynn’s prior admissions in court as “powerful evidence” against him.

The judge wrote: “Asserting factual bases that are irrelevant to the legal standard, failing to explain the government’s disavowal of evidence in the record in this case, citing evidence that lacks probative value, failing to take into account the nature of Mr. Flynn’s position and his responsibilities, and failing to address powerful evidence available to the government likely do not meet” the legal standard that would have led him to dismiss the case.

But Mr. Trump’s constitutional pardon power is broad and clearly covered the matters pending before him, Judge Sullivan added — so he was ending the case. At the same time, he stressed, that does not render Mr. Flynn “innocent” of the allegations against him.

Katie Benner contributed reporting.