The office headed by the woman poised to become the next attorney general has used an unusual method to keep many of its prosecutions hidden from the public, an NBC News investigation has found.

Federal prosecutors in New York’s Brooklyn-based Eastern District pursued cases against secret, unnamed “John Doe” defendants 58 times since Loretta Lynch became head prosecutor in May 2010. Two of the 58 are terrorism cases.

Eastern District prosecutors have also sought permission to close the courtroom to the public for 11 different Doe cases during the same period, and judges have granted permission in at least 10 of the cases, as recently as February 12.

Critics are concerned the practice may infringe the Constitution’s guarantee of a public trial.

“While pseudonyms may be appropriate in exceptional cases, the courts should always opt for more transparent methods of protecting sensitive information when available,” said Lee Rowland, staff attorney of the ACLU Speech, Privacy & Technology Project. “The disproportionate number of John Doe cases in the Eastern District is certainly a cause for concern; complete secrecy about the parties in a case should never be a default option.”

On November 8, 2014, President Obama nominated Lynch to succeed Eric Holder as Attorney General. The Senate Judiciary Committee questioned Lynch during confirmation hearings in January, and the committee’s vote on her confirmation is scheduled for Thursday. Lynch is in her second stint as head prosecutor in Brooklyn, also serving as the Eastern District’s U.S. Attorney from 1999 to 2001.

Federal prosecutors around the country use a variety of techniques to keep the identities of defendants secret, often to protect cooperating witnesses or to help secure a plea deal. Methods include filing cases under seal to keep them off court dockets, or sealing the identities of some secondary defendants who have become cooperating witnesses.

The Eastern District’s use of John Doe, however, is conspicuous. None of the nation’s 93 other federal district courts has charged more than eight “Does” during the same time period, and the national average is under four. * In the two federal districts with similar pending criminal caseloads (approximately 3000 cases) -- Arizona and the Southern District of California -- there is only one case involving a “John Doe” defendant.

The alleged offenses prosecuted in the Brooklyn Doe cases include everything from drug trafficking, violent crimes, fraud and hacking to terrorism.

Brian Fallon, director of public affairs for the Justice Department, cited “safety and security in ongoing matters” as the motives for the Eastern District’s Doe designations, and said that after “supervisory approval and review” with the U.S. Attorney’s office, the Doe label must be approved by the court as well.

“To the extent the number of 'John Doe' filings may be higher in the Eastern District of New York than other districts,” said Fallon, “the office's docket of terror cases and other violent crime matters is likely a contributing factor. It is also likely the case that other districts are more likely to file their cases completely under seal rather than file 'John Doe' cases."

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On Wednesday, the Eastern District announced the arrest of three named defendants for allegedly plotting to wage jihad for ISIS. Prosecutors identified the defendants as Abdurasul Juraboev, 24, Akhror Saidakhmetov, 19, and Abror Habibov, 30, all of Brooklyn.

But in an Eastern District case from August 2014, a “John Doe” pleaded guilty in a closed courtroom to terrorism charges, including the receipt of “military-type” training and the illegal use of firearms. That case and another Brooklyn case from January 2013 are the only docketed federal terrorism cases in the country where the defendants’ identities have been concealed.

Don Borelli, COO of the Soufan Group and former assistant special agent in charge of the New York Joint Terrorism Task Force (JTTF), believes the practice stems from the Eastern District’s proactive approach to fighting terror. “The Eastern District, number one, is very aggressive. They have a lot of experience with terrorism,” said Borelli, who is also an NBC News analyst. “I’m not surprised they’re leading the pack in some of these things.”

The real identities of defendants in other districts’ sealed cases generally become public once the indictments are ordered unsealed by the judge. In the Eastern District Doe cases, the true identities have been revealed when defendants are sentenced –- but only three of the 58 defendants have a public record of sentencing, even though sentencing dates for many others have passed. In 40 of the 58 cases, many of the related court documents are sealed as well.

“The Non-Public Nature of the Investigation Is Crucial To Its Success”

In the U.S. justice system, “John Doe” designations are sometimes used to protect juveniles. One of the Brooklyn Does was a juvenile. The Doe tag can also be used when identities are not certain. Such cases often list aliases or possible real names for the defendant in addition to “John Doe.” Five of the 58 Eastern District Doe cases list these possible real names.

As Fallon indicated, the “Doe” label can also be employed to protect the identities of defendants when national security is said to be at stake.

Court records show that Eastern District prosecutors used the national security argument to convince a judge to preserve the Doe designation and keep the courtroom sealed in at least one instance, the 2014 terrorism case.

Judge Pamela K. Chen revealed the government’s argument when she denied a reporter’s motion to open the courtroom, unseal the case and reveal the defendant’s identity.

In her October 30, 2014 order upholding the “Doe” designation, she wrote, “the Government’s investigation involves national security issues and the non-public nature of the investigation is crucial to its success...unsealing this matter could jeopardize the safety of numerous individuals...both the closure of the proceedings and the sealing of the record were narrowly tailored to protect the law enforcement interests at stake in this matter.” **

The defendant in the 2014 terror case pleaded guilty to terrorism and military training charges and is awaiting sentencing. Lynch’s office would not comment on whether the defendant is free on bond pending sentencing, or is in U.S. custody.

“With terrorism you're dealing with national security,” said Borelli. “You have a whole other playbook when you’re dealing with terrorism. … If the investigation is ongoing, you can’t play all of your cards face up at that point.”

Two of the federal jurisdictions with the most significant track records of trying terror and organized crime cases do not use the Doe designation as frequently as the Eastern District, and haven’t used them for terror cases.

Since January 1, 2010 the U.S. Attorney’s offices in the Southern District of New York and Eastern District of Virginia have pursued only five John Doe cases combined. In each of those cases, which were on child pornography, immigration, and narcotics charges, the “John Doe” designation appeared in the docket next to the defendant’s alias -– meaning an unconfirmed or suspected name or nickname.

All but two of the Eastern District’s Doe cases, meanwhile, are for non-terror-related crimes.

The Doe designation can also be used when a cooperating witness has accepted a plea agreement and consented to the use of a pseudonym.

Critics suggest that while a promise of anonymity may be an effective bargaining tool, and may satisfy the defendant, such plea deals keep the public in the dark.

Three of the Eastern District Does prosecuted since May 2010 have been sentenced, and had their true identities revealed. Defendants in two cases have not yet entered pleas. Twenty-two other cases have a scheduled sentencing date, but most of those dates have already passed. Thirty-one cases have no sentencing records at all.

In a recent essay for the New York Review of Books, a federal judge warned about the secrecy that surrounds plea bargaining, and said that such a system “invites arbitrary results.’

“There is a great irony,” wrote Judge Jed Rakoff, ”in the fact that legislative measures that were designed to rectify the perceived evils of disparity and arbitrariness in sentencing have empowered prosecutors to preside over a plea-bargaining system that is so secretive and without rules that we do not even know whether or not it operates in an arbitrary manner.”

*A note on methodology: Data is based on analysis of all federal criminal cases filed from May 1, 2010 to the present from all 94 federal district courts that were entered into Pacer, a publicly available database of federal court records. No distinction was made between busy districts and courts with relatively light caseloads. All defendants in Pacer named John, Jane or J. Doe are included, and any defendants with the real name Doe were removed.

**Full disclosure: This reporter requested that the court unseal the case, reveal the suspect’s identity and open the courtroom and is currently appealing Chen’s ruling to the 2nd Circuit.