Former CIA director George Tenet has acknowledged that elements of the counterintelligence investigation against a former Jewish attorney at the agency in the 1990s could be construed as anti-Semitic.

Tenet acknowledged this in a previously undisclosed sworn deposition, part of a privacy act lawsuit filed by the former attorney, Adam Ciralsky. In 1999, Ciralsky’s security clearance was revoked because of his alleged lack of candor about contact with Israelis and Israeli-Americans, effectively ending his brief career with the CIA. For the last dozen years Ciralsky has sued the CIA to bring to light how he believes a few agency officials—motivated by anti-Semitism—targeted him unfairly. On Friday he dropped his case.

“I am proud of my service with the CIA and have a deep and abiding respect for the organization and its mission,” Ciralsky said in a statement. “I am equally proud that by highlighting and confronting the misconduct of a few, I spurred positive change.”

While Tenet acknowledged in a 1999 letter to the Anti-Defamation League that some of the conduct of CIA investigators in the Ciralsky case was inappropriate, Tenet goes further and into more detail in the new deposition. Tenet authorized sensitivity training for the CIA on anti-Semitism following allegations of misconduct in the Ciralsky investigation. At the time the CIA said Ciralsky’s dismissal was not the result of anti-Jewish prejudice.

According to the transcript of a 2010 deposition viewed exclusively by The Daily Beast, Tenet said statements attributed to an officer who administered a polygraph to Ciralsky were “insensitive, inappropriate and unprofessional”—and could be construed as anti-Semitic.

The statement in question was from a polygraph administrator identified as “Charles B” in the court transcripts. In a sworn declaration, another CIA polygraph administrator, John Sullivan said, “I was in B’s office when he came and I asked him how the test was going. B’s response was to refer to Ciralsky as ‘that little Jew bastard.’ I don’t recall what B said after that but I believe that he said something to the effect that he, B, ‘knew Ciralsky was hiding something.’”

When Tenet was asked about Sullivan’s affidavit, he said, “Well it’s insensitive, inappropriate and unprofessional and I would want and I would have wanted to talk to this guy to find out what the context was and whether he said it or not.”

Tenet was then asked if the polygraph administrator’s comments were anti-Semitic. Tenet responded, “I don’t know the individual in question. It could be construed that way.”

The comments from the CIA polygraph administrator were not the only elements of the investigation into Ciralsky that appeared inappropriate. His internal CIA file, for example, notes that he failed to disclose how he is related to former Israeli president Chaim Weizmann and speculated that his parents gave money to pro-Israel causes. The file also described Ciralsky as a “rich Jewish employee with a wealthy daddy.” When Tenet was asked whether it was appropriate to describe Ciralsky that way, Tenet answered, “No.”

The fact that Ciralsky’s lawyers were able to depose Tenet for the court is nearly unprecedented. CIA directors rarely offer depositions in civil cases brought by former employees.

“I think it’s unprecedented. I have never heard of anything like this before,” said Victoria Toensing, a former chief counsel for the Senate Select Committee on Intelligence and an attorney who has taken high profile cases against the agency in the past.

“Usually the agency tries to circle the wagons and protect the director from ever having to provide facts,” Toensing said. “The fact that he was privy to the gross violations that occurred here is what is significant. That he was aware of the abuse that occurred is significant. And you have to give him credit for acknowledging it.”

In the course of his deposition, Tenet was asked about whether he said in a senior staff meeting that because Ciralsky was not candid he was “outta here.” The only problem was that Tenet made those remarks two weeks before the actual polygraph test. When asked about the remarks, Tenet said he never said it and suggested the note taker in the meeting got it wrong.

Since a Navy analyst named Jonathan Pollard was discovered spying for Israel in 1985, Jewish Americans working in the intelligence and defense bureaucracy have complained of increased scrutiny by counterintelligence officers. While Israel’s Mossad and the CIA cooperate closely, particularly on Iran, the FBI has also in recent years warned that Israel is one of the most aggressive recruiters of agents in the United States, along with China and Russia.

In 2008 at a speech at the Anti-Defamation League (ADL), Tenet acknowledged that there were elements of the agency that had an anti-Jewish prejudice.

“We had a problem once at CIA,” he said in that speech. “There is no doubt that there was anti-Semitism at stake. With the help of ADL trainers we educated an entire bureaucracy and taught people about how their words could be misinterpreted in a manner that was detrimental to the interests of the country.”

A CIA spokesman when asked for comment Friday said, “Although the CIA does not comment on any specific matters pending before the courts, the agency has, and enforces, a well-publicized zero-tolerance policy on discrimination.”