ATLANTA — In an embarrassing blow to the prosecutor investigating election interference by former President Donald J. Trump, an Atlanta judge has disqualified District Attorney Fani T. Willis of Fulton County from developing a criminal case against one Trump ally, citing a conflict of interest.
Ms. Willis had recently notified State Senator Burt Jones, the Republican candidate for lieutenant governor in Georgia, that he could face indictment. But on Monday, Judge Robert C.I. McBurney of Fulton County Superior Court barred her from pursuing a case against Mr. Jones because she had headlined a June fund-raiser for his Democratic rival in the race.
Mr. Jones was one of 16 pro-Trump “alternate electors” in Georgia who were sworn in on the same day as the state’s legitimate presidential electors, who cast their votes for Joseph R. Biden Jr. Ms. Willis’s office had recently warned the pro-Trump electors, as well as another state senator and the head of the Georgia Republican Party, that they could face charges in the matter.
The ruling on Monday does not affect any other portion of the sprawling investigation that Ms. Willis’s office is conducting with a special-purpose grand jury. Even so, it underscores the complicated political terrain that lies before Ms. Willis, a first-term Democrat.
“She has bestowed her office’s imprimatur upon Senator Jones’s opponent,” Judge McBurney wrote in his decision. He added: “This scenario creates a plain — and actual and untenable — conflict. Any decision the district attorney makes about Senator Jones in connection with the grand jury investigation is necessarily infected by it.”
The ruling does not mean that Mr. Jones cannot be investigated. Ms. Willis’s office, the judge wrote, will still be able to ask witnesses about Mr. Jones’s role “in the various efforts the state Republican Party undertook to call into question the legitimacy of the results of the election.” However, he wrote, the decision “as to whether any charges should be brought, and what they should be, will be left to a different prosecutor’s office.”
The choice of a new prosecutor to evaluate whether any charges should be brought against Mr. Jones will eventually be made by the Prosecuting Attorneys’ Council of Georgia, a group that sets policies and rules for district attorneys around the state.
Peter J. Skandalakis, the executive director of the group, said in a statement on Monday that “it may be best” to wait until the special grand jury finishes its work before getting another prosecutor involved. He noted that Ms. Willis could no longer call Mr. Jones as a witness or issue subpoenas for his documents. But he said that the special grand jury, which will issue an advisory report after meeting for up to one year, may continue to investigate Mr. Jones’s conduct.
Ms. Willis’s lawyer had argued that the fund-raiser she headlined for Charlie Bailey, the Democratic candidate for lieutenant governor, took place during a primary runoff between two Democratic candidates, and that a mailer for the event clearly showed it was related to the runoff, not the general election contest against Mr. Jones.
The judge acknowledged that those facts were “rightly” pointed out, but he said what was “more relevant — and harmful — to the integrity of the grand jury investigation is that the die was already cast on the other side of the political divide,” and that whoever won the runoff “would face Senator Jones.”
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The ruling came a few days after Judge McBurney criticized Ms. Willis in a hearing last week for her participation in the fund-raiser, calling it a “what-are-you-thinking moment.” The judge also expressed concern that the district attorney, as “the legal adviser to the grand jury,” was “on national media almost nightly talking about this investigation.”
While the House select committee in Washington that is investigating the Jan. 6, 2021, attack on the Capitol has put on display how Mr. Trump and his allies sought to subvert the election results in several crucial states, it is Ms. Willis’s investigation that puts Mr. Trump and his allies in the most immediate legal peril.
The judge’s ruling concerning Mr. Jones is likely to have limited repercussions for Ms. Willis’s broader investigation, since the ruling concerns only one of the 16 pro-Trump purported electors.
Jeff DiSantis, a deputy district attorney for Fulton County and a spokesman for Ms. Willis, said on Monday that the office was reviewing the order and “considering a potential course of action.”
The Georgia investigation is gaining increasing attention as it engulfs more of Mr. Trump’s allies and advisers. Mr. Trump’s personal lawyer, the former New York City mayor Rudolph W. Giuliani, has been ordered by a judge to testify on Aug. 9. Lawyers for Senator Lindsey Graham of South Carolina are fighting efforts to compel him to testify.
Ms. Willis is also seeking to compel testimony from John Eastman, an architect of the legal strategy intended to keep Mr. Trump in power, as well as other lawyers — Kenneth Chesebro, Jacki Pick Deason, Jenna Ellis and Cleta Mitchell — who played important roles in the effort.
Eleven of the other pro-Trump purported electors in Georgia asked the Judge McBurney to have Ms. Willis disqualified from investigating them as well, but the judge denied their motion, saying that none of them had shown that Ms. Willis’s office was “impaired by a conflict of interest” in their cases. The judge also denied their effort to quash the subpoenas they received.
The pro-Trump purported electors are slated to appear later this week before the special grand jury, which is meeting behind closed doors in a downtown Atlanta courthouse.
The fact that Mr. Jones could face indictment has injected a measure of drama into the lieutenant governor’s race in Georgia, one of several races that are being closely watched nationwide in the battleground Southern state. Mr. Bailey, a lawyer who formerly worked with Ms. Willis in the district attorney’s office, has accused Mr. Jones of participating in a “failed attempted overthrow of the American Government.”
Mr. Jones said in a statement on Monday that the judge’s ruling was a “huge win” for him, and accused Mr. Bailey of running a “smear campaign.”
In a separate matter on Monday, a federal judge said that she would reject an effort by United States Representative Jody Hice to skirt a subpoena asking him to give testimony before the special grand jury. Mr. Hice, a Georgia Republican and staunch Trump ally, led a January 2021 challenge in the House of Representatives to the certification of Georgia’s electors.
Mr. Hice’s lawyers had argued that he did not have to comply with the subpoena because, in part, of protections afforded to members of Congress by the Speech and Debate clause of the Constitution.
Though U.S. District Court Judge Leigh Martin May said that Mr. Hice would have to testify, she also said that some limits could be set on what he would be compelled to discuss. That matter, she said, would be hashed out by lawyers at an upcoming court date.