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Just Anticorruption
Meet AP Leak Prosecutor Jonathan Malis: Investigating Journalists and Butting Heads with Holder
By Jennifer Koons and Mary Jacoby | May 20, 2022 4:18 pm

One of the prosecutors who sought two months of telephone records from the Associated Press in a leak probe – sparking an uproar over First Amendment rights – has a history of aggressive pursuit of high-profile national security cases marked by controversy.

Assistant U.S. Attorneys Ken Kohl (l) and Jon Malis (r) in Baghdad in 2007 (Getty).

Assistant U.S. Attorney Jonathan Malis in the District of Columbia butted heads with then-private defense lawyer Eric Holder in his 2007 successful prosecution of Chiquita Brands International for making prohibited payments to a terrorist group in Colombia.

Malis is on the prosecution team that investigated Fox News journalist James Rosen in connection with the 2010 indictment of a government contractor accused of leaking classified information about North Korea.

And he was among the prosecutors accused by a federal judge of using tainted evidence against four former guards for Blackwater Worldwide who had been accused of shooting Iraqi civilians in Baghdad’s Nisour Square in 2007. An appeals court overruled the district court judge, and an internal Justice Department review cleared Malis.

In each case, Malis showed himself to be an extremely aggressive prosecutor unbowed by criticism and controversy, and unmoved by nuance. But his positions ultimately prevailed.


The Chiquita case was notable for Malis’s insistence that lawyers for the banana company expand an already agreed upon waiver of attorney-client privilege, a practice that has since been reined in by the Justice Department.

Chiquita had been in an unusual situation. The company had been extorted by the Self-Defense Forces of Colombia (AUC), designated as terrorists by the United States for widespread human rights abuses and killings. The right-wing paramilitary group had threatened to kill the company’s employees if it didn’t receive payments from Chiquita.

View Main Justice's multi-media presentation of the Chiquita Banana case.

Chiquita belatedly realized the extortion payments were illegal when it discovered that the AUC had been placed on a designated terrorist list by the United States.

The company self-disclosed the payments to the Justice Department, but received unclear guidance from then-Criminal Division chief Michael Chertoff about whether it must stop the payments.

After strong-arming the company to expand its attorney-client privilege waiver, Malis learned some damning evidence: its outside counsel, Kirkland & Ellis LLP, had told the company in no uncertain terms that the payments were illegal and had to stop. But the company’s then-general counsel, fearing violence, allowed them to continue, according to a special report of the matter commissioned by the company’s audit committee.

Kirkland was conflicted out of the case – its lawyers were now potential witnesses against Chiquita. Holder, then a defense lawyer at Covington & Burling LLP, stepped in to negotiate a settlement.

Holder’s initial offer of $1 million to settle was met by Malis’s counter-offer of $79 million – and his insistence the company plead to a relatively more serious charge of providing “material support” to a terrorist group.

Holder then went over Malis’s head. Then-D.C. U.S. Attorney Jeffrey Taylor and others at Main Justice reined Malis in. Chiquita ultimately pleaded guilty to a lessor offense and agreed to pay $25 million over five years.

During Chiquita’s Sept. 17, 2007, sentencing hearing, Holder condemned Malis’s approach to the case as “not worthy of the office he represents.” Holder said that when he served as the department’s number two official during the Clinton administration, “heads would have rolled” had the DOJ not given Chiquita clear guidance on the Colombian payments.

“I am not going to respond to what I view as the ad hominem attack on this prosecutor,” Malis replied, according to The Daily Beast.

Criminal investigation of Fox News reporter

Malis is one of the prosecutors who investigated Fox News reporter James Rosen as a potential criminal conspirator for publishing a June 2009 article discussing the likelihood of North Korea conducting nuclear tests.

A federal grand jury in 2010 indicted Rosen’s alleged source, Stephen Jin-Woo Kim, a former government contractor stationed at the State Department, for leaking classified information that appeared in Rosen’s report.

Fox News reporter James Rosen

Court records show that in 2010, the FBI sought court approval for a search warrant for Google Inc. to obtain the gmail account of a journalist later identified Rosen. The affidavit says the U.S. had reason to believe Rosen may be criminally liable under a statute, 18 U.S.C. § 793, which makes it illegal to disclose information that could harm national security. The maximum penalty for a violation is 10 years in prison.

The FBI used Rosen and Kim’s security-badge data to check their comings and goings at the State Department, establishing strong evidence of a face-to-face meeting shortly before Rosen published his account.

The affidavit for the search warrant also describes their somewhat bumbling attempts to hide the relationship - Kim is alleged to have used the pseudonym “Leo” in personal account email communications with Rosen, who used the name “Alex,” an apparent reference to Watergate figure Alexander Butterfield, who ran President Richard Nixon’s secret Oval Office recordings. Yet, the affidavit notes, in one emailed signed “Alex,” Rosen’s full name, address, phone number and news organization appear below in his signature box.

Kim’s defense lawyer, Abbe Lowell, has argued that it’s not a crime to speak with reporters.

Kim’s case is pending in federal district court in Washington, D.C. The status of the investigation into Rosen isn’t clear, but he has not been charged.


Malis was singled out by U.S. District Judge Ricardo Urbina in a Dec. 31, 2009 ruling that accused prosecutors of violating the constitutional rights of the former Blackwater Worldwide security guards acccused in the Iraq shootings. (See Main Justice’s report here.)

Ricardo Urbina

He was part of a prosecution team lead by Assistant U.S. Attorney Ken Kohl that inherited a flawed case from the State Department. The guards had given what Judge Urbina determined to be compelled testimony to State Department investigators after the shooting incident in Baghdad, which left more than 30 Iraqi civilians dead or injured.

Under extreme political pressure by Iraq to prosecute the guards, the Justice Department tried to work around the compelled testimony problem. But Malis and other prosecutors were stymied in part because some of the former guards’ statements had been leaked to the media, where they became widely known, making it difficult to sort out what the guards knew first-hand from what they’d read.

In “their zeal to bring charges,” prosecutors “purposely flouted” repeated warnings of a Justice Department “taint team” not to rely on compelled statements from the guards, Judge Urbina wrote.

But the U.S. Court of Appeals for the D.C. Circuit overturned Urbina’s ruling, and the case, with a new team of prosecutors, went forward.

The District of Columbia U.S. Attorney’s Office provided a letter to Main Justice sent to Malis on May 1 from the Executive Office for United States Attorneys. The letter notifies Malis that he has been found not to have demonstrated professional misconduct or poor judgment in the Blackwater case

Associated Press case

In the Associated Press case, the Justice Department has been roundly criticized for its decision to subpoena two months of cellular, office and home telephone records of AP reporters in New York, Washington, and Hartford, Conn., apparently as part of a probe into the leak of news about a foiled plot by Al Qaeda’s affiliate in Yemen to bomb a U.S.-bound jetliner.

But a former prosecutor who has worked with Malis in the past told The Daily Beast that the Assistant U.S. Attorney is unlikely to be “shedding any tears for the Fourth Estate.”

Bill Miller, a spokesman for the U.S. Attorney’s office, said of the AP probe: “All laws, policies and procedures were followed, including multiple layers of review at the U.S Attorney’s Office and the Department of Justice.”

Holder, who as Attorney General normally would have been required to approve any subpoena of the news media, was recused because the FBI had interviewed him, apparently as a potential source for the leak.

With Holder recused, Deputy Attorney General James Cole signed off on the subpoenas.

The New York Times later identified Malis as the prosecutor who notified the AP reporters that their phone records had been secretly subpoenaed. Miller of the U.S. Attorney’s office said Malis “was one of many people on this case.” He noted: “There were multiple layers of review that went beyond Mr. Malis and the prosecution team.”

Appearing on CBS’ “Face the Nation” on Sunday, AP chief Gary Pruitt called the seizure “unconstitutional.”In a separate interview with the AP, Pruitt said the news wire had not decided whether it would take legal action.

This article was updated to add further comments from the D.C. U.S. Attorney’s office and to include an internal Justice Department letter provided by spokesman Bill Miller clearing Malis of misconduct in the Blackwater case.


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"I'm a Verizon customer, it doesn't bother me one bit for the National Security Administration to have my phone number." -- Sen. Lindsey Graham (R-S.C.)