The judge’s comments, made while the jury was out of the courtroom, were part of a ruling denying Mr. Atilla’s request for a mistrial on the grounds that the government’s evidence had not been properly authenticated and was highly prejudicial.
In denying the request for a mistrial, the judge rejected the defense’s claims. “In my judgment,” he said, “Mr. Atilla has received and is receiving a thoroughly fair and transparent trial.”
The judge’s allusions to the Gulenist issue, however, seemed to underscore the extraordinary nature of the case, which has sent political tremors through Turkey and riveted the public there.
The judge focused his criticism on the cross-examination of a former Turkish police officer, Huseyin Korkmaz, who fled Turkey last year with evidence from a 2013 Turkish corruption investigation that he had supervised, which he later gave to United States authorities.
Turkish officials had quashed the 2013 police investigation and jailed Mr. Korkmaz for a time, the jury has been told.
In one exchange during the cross-examination that the judge cited critically, a defense lawyer, Todd Harrison, noted that Mr. Korkmaz had been freed from prison after a Turkish judge received a letter from Mr. Gulen, asking that Mr. Atilla and others be released.
“Correct?” Mr. Harrison asked.
“This sounds very illogical to me,” Mr. Korkmaz responded, denying that he knew Mr. Gulen or the Turkish judge.
Judge Berman also cited questions in which he said Mr. Harrison appeared to be arguing that Mr. Korkmaz’s police promotions were mostly the result of “alleged Gulenist backing.”
The judge said the defense’s “illogical foreign conspiracy theory has no foundation in the record, and is, in reality, unpersuasive and borderline unprofessional, as a diversion from the issues to be decided in this case.”
Mr. Harrison, asked later for comment, said: “I disagree. I think it was legitimate cross-examination.”
Earlier Friday, Michael D. Lockard, an assistant United States attorney, announced that the prosecution was resting its case.
After the defense began its presentation, Mr. Atilla started testifying, a decision the defense revealed late Thursday.
Another defense lawyer, Cathy Fleming, asked him, “Did you conspire with Reza Zarrab to evade sanctions?”
“Never,” Mr. Atilla said through an interpreter.
“Did you intend to defraud any banks?”
“Never,” he repeated.
Ms. Fleming posed several other such questions, drawing much the same response.
“Are you the architect of the schemes that Mr. Zarrab drew for this jury?” she asked, referring to a diagram Mr. Zarrab sketched when he was on the witness stand.
“I’m not,” Mr. Attila said.