WASHINGTON — During Gina Haspel’s confirmation hearing to become director of the C.I.A. in 2018, Senator Dianne Feinstein asked her if she had overseen the interrogations of a Saudi prisoner, Abd al-Rahim al-Nashiri, which included the use of a waterboard.
Ms. Haspel declined to answer, saying it was part of her classified career.
While there has been reporting about her oversight of a C.I.A. black site in Thailand where Mr. Nashiri was waterboarded, and where Ms. Haspel wrote or authorized memos about his torture, the precise details of her work as the chief of base, the C.I.A. officer who oversaw the prison, have been shrouded in official secrecy.
But testimony at a hearing last month in Guantánamo Bay, Cuba, included a revelation about the former C.I.A. director’s long and secretive career. James E. Mitchell, a psychologist who helped develop the agency’s interrogation program, testified that the chief of base at the time, whom he referred to as Z9A in accordance with court rules, watched while he and a teammate subjected Mr. Nashiri to “enhanced interrogation” that included waterboarding at the black site.
Z9A is the code name used in court for Ms. Haspel.
The C.I.A. has never acknowledged Ms. Haspel’s work at the black site, and the use of the code name represented the court’s acceptance of an agency policy of not acknowledging state secrets — even those that have already been spilled. Former officials long ago revealed that she ran the black site in Thailand from October 2002 until December 2002, during the time Mr. Nashiri was being tortured, which Dr. Mitchell described in his testimony.
Guantánamo Bay is one of the few places where America is still wrestling with the legacy of torture in the aftermath of the Sept. 11, 2001, attacks. Torture has loomed over the pretrial phase of the death penalty cases for years and is likely to continue to do so as hearings resume over the summer.
Defense teams have been asking military judges to exclude certain evidence from the war crimes trials of accused Qaeda operatives as tainted by not just torture but also cruel, inhuman and degrading treatment. In May, that meant revisiting what happened nearly 20 years ago at the secret prison in Thailand.
Dr. Mitchell described how in late 2002 he and another C.I.A. contract psychologist, John Bruce Jessen, waterboarded Mr. Nashiri, who is accused of orchestrating the bombing of the Navy destroyer Cole in 2000. Seventeen American sailors were killed in the attack.
During three separate sessions, Dr. Mitchell held a cloth over the man’s face and adjusted it to direct the water as Dr. Jessen poured.
Dr. Mitchell testified that Mr. Nashiri was so small that they thought he might slide out of his Velcro restraints during portions of the waterboarding. To let Mr. Nashiri breathe between pours, interrogators pivoted him 90 degrees, from lying on his back to a standing position, still strapped to a gurney.
The interrogation team shifted to other “coercive techniques,” including forcing the prisoner to spend time in a small confinement box. Dr. Mitchell said he had a “general memory of what was done” — the detainee, who was nude and sometimes hooded, was probably slapped and had the back of his head slammed into a burlap-covered wall — but testified that he did not have a “blow-by-blow recollection of any of that stuff.”
It was previously known that by the time Mr. Nashiri was waterboarded in late 2002, Ms. Haspel had taken over as the chief of base at the secret prison in Thailand. It has also been reported that she drafted cables relating what happened to Mr. Nashiri and what was learned during his interrogations and debriefings.
But Dr. Mitchell’s testimony went further. He testified that the chief of base observed the sessions, though she did not participate in them.
The law firm that employs Ms. Haspel, King & Spalding L.L.P., declined to comment and referred questions to the C.I.A., which also declined to comment.
Dr. Mitchell never mentioned the person by name. Instead, because she was serving in a clandestine role at the time, he was required to refer to the chief of base as Z9A, or, as one lawyer sounded it out, “Zulu Nine Alpha.”
The codes are part of the choreography of the hearings at Guantánamo Bay, where the court has a mute button to protect against inadvertent disclosures of classified information and prosecutors work with the C.I.A. to keep official secrets out of the public record.
Prosecutors in the death-penalty cases, working with members of the intelligence community, assigned alphanumeric codes to most C.I.A. staff members who worked at the black sites. Nations where the C.I.A. had prisons are referred to by numbers. For Dr. Mitchell’s hearing, prosecutors provided him with a secret list of names and alphanumerics — a key of sorts that lawyers in court called “a crosswalk.”
For example, Dr. Mitchell referred to the agency’s chief interrogator in 2002, who died not long after he oversaw some of Mr. Nashiri’s harshest interrogations, as NX2.
And although Ms. Haspel’s role as chief of base at the black site in Thailand is widely known, it is still considered a state secret.
The judge, Col. Lanny J. Acosta Jr., agreed to allow Dr. Mitchell to testify because the C.I.A. had destroyed videotapes that defense lawyers argue showed the psychologists torturing and interrogating Mr. Nashiri and another prisoner at the black site in Thailand. Defense lawyers said that deprived them of potential evidence, including something they might have wanted to show a military jury deciding whether to impose a death penalty.
The disclosure that the C.I.A. had destroyed the tapes — most of them showing Abu Zubaydah, the first detainee taken into custody and known to be tortured by the C.I.A. after the Sept. 11 attacks — prompted the Senate Intelligence Committee to investigate the black site program.
Ms. Haspel has acknowledged her role in the destruction of those tapes as a chief of staff to the operations chief, Jose A. Rodriguez Jr. At her confirmation hearing, she said, “I would also make clear that I did not appear on the tapes.”
Observers at the site in Thailand watched waterboarding and other interrogations via a closed-circuit video feed to a separate room. At one point, the C.I.A. sent some staff members to the black site to watch the waterboarding of Abu Zubaydah. But, Dr. Mitchell testified, Ms. Haspel was not among them.
The Senate Intelligence Committee study of the C.I.A. program, only a part of which is public, said that interrogators wanted to stop using “enhanced interrogation techniques” on Mr. Nashiri because he was answering direct questions, but they were overruled by headquarters.
Mr. Nashiri would also be tortured later, after Dr. Mitchell had taken him to a different C.I.A. black site. Another interrogator revved a drill next to the naked detainee’s hooded head, apparently to try to get him to divulge Qaeda plots. At another black site in 2004, the C.I.A. infused a dietary supplement into his rectum for refusing to eat. His Navy lawyer has called the procedure rape.
At her confirmation hearing, Ms. Haspel pledged not to set up any similar interrogation programs.