WASHINGTON — A federal judge on Tuesday threw out the conviction of a business associate of the former national security adviser Michael T. Flynn, saying prosecutors had failed to offer enough evidence to sustain their charges that he had secretly lobbied on behalf of Turkey.
Judge Anthony J. Trenga of the United States District Court for the Eastern District of Virginia wrote in a lengthy opinion that there was no evidence of “any actual or implied agreement” between Mr. Flynn’s partner, Bijan Kian, and the government of Turkey. “The government has failed to offer substantial evidence from which any rational juror could find beyond a reasonable doubt” that Mr. Kian had acted as an agent of a foreign power without notifying the Justice Department as required by law, Judge Trenga said.
The judge’s decision, overturning a jury’s July verdict, delivered a potentially fatal blow to the government’s efforts to prosecute Mr. Kian in a case that had already suffered other setbacks.
Mr. Flynn, a central figure in the case, had abruptly changed his story before the trial, prompting prosecutors to scrap him as a witness. And after defense lawyers asked the court to toss the case before it went to the jury, Judge Trenga considered the motion, describing the case as speculative and circumstantial. But he let the trial move forward, and the jury quickly convicted Mr. Kian on two counts: conspiracy to violate lobbying laws and failure to register as a foreign agent.
“Bijan and his family are relieved and looking forward to getting on with their lives,” said Mark MacDougall, a lawyer for Mr. Kian. “We are all grateful to the court. Our system is still sturdy and, in this case, justice has been done.”
A spokesman for the United States attorney’s office said prosecutors were reviewing the court’s opinion and declined to comment further.
Judge Trenga said that if his decision were vacated or reversed by a higher court, a “new trial is warranted in the interests of justice.”
Defense lawyers had relentlessly attacked the government’s case against Mr. Kian, asserting there was no actual agreement with the Turkish government to influence American policy. Mr. Kian’s lawyers said prosecutors could not even show that Turkey paid for anything. Mr. Kian was on the Trump transition team and worked on national security matters.
Prosecutors indicted Mr. Kian in December, along with another man, Ekim Alptekin, as part of an investigation into Turkey’s secret 2016 lobbying campaign to pressure the United States to expel Fethullah Gulen, a rival of President Recep Tayyip Erdogan’s.
Prosecutors accused Mr. Kian and Mr. Alptekin of trying to hide the role of Turkish government officials who were directing the project. Mr. Flynn’s firm, Flynn Intel Group, received a total of $530,000 for its work on the effort.
Nothing Mr. Alptekin said to Mr. Kian “was sufficient for a rational juror to find” that Mr. Kian “had agreed to act or was knowingly acting as an agent of the Turkish government.” The judge said there was no evidence that the men were “channeling instructions from the Turkish government concerning the day-to-day operational details of that work.”
Mr. Flynn had been expected to help prosecutors establish their case. But on the eve of the trial, Mr. Flynn blamed his previous lawyers for filing inaccurate foreign lobbying disclosure forms without his knowledge. Prosecutors then decided not to call him as a witness, playing down the import of his testimony and contending he was not part of the conspiracy involving Mr. Kian.
Mr. Flynn had previously admitted that he had lied on foreign lobbying disclosure forms submitted to the Justice Department.
In his decision, Judge Trenga pointed to prosecutors’ decision to begin examining whether Mr. Flynn was working as a paid lobbyist for Turkey after he wrote an op-ed for The Hill newspaper on Election Day 2016 attacking Mr. Gulen as a “radical Islamist” and a “shady Islamic mullah.”
Judge Trenga said there was “no evidence that the op-ed had been requested by the Turkish government.”
As for the conspiracy charge, Judge Trenga said the government failed to present “sufficient evidence” Mr. Kian conspired with Mr. Alptekin or anybody else.
It is not clear what effect the judge’s decision will have on Mr. Flynn, who had delayed his sentencing to maximize his cooperation in Mr. Kian’s case. Mr. Flynn has admitted to lying to F.B.I. agents about conversations he had during the presidential transition in late 2016 with the Russian ambassador, Sergey I. Kislyak.
Mr. Flynn is tentatively scheduled to be sentenced in December. Prosecutors have hinted that they will ask for prison time after originally recommending probation.
The decision is the most recent blow to federal prosecutors trying to crack down on violations of the Foreign Agents Registration Act, which requires people lobbying the government on behalf of foreign nations to notify the Justice Department.
This month, prosecutors in the District of Columbia lost a high-profile case against Gregory B. Craig, one of Washington’s most prominent Democratic lawyers. He was acquitted of a felony charge of lying to federal authorities about work he did years ago for the Ukrainian government.