Several months ago, Jann Wenner, a founder of Rolling Stone magazine, received a call from the actor Sean Penn.
Mr. Penn, Mr. Wenner said in an interview on Sunday, wanted to discuss something important. But he did not want to speak openly over the phone, so the two began to speak elliptically about a potential project.
That vague conversation was the beginning of what eventually became an article, written by Mr. Penn, that rocked both Mexico and the United States when it was published Saturday night. It was an exclusive interview with Joaquín Guzmán Loera, the notorious drug kingpin known as El Chapo, that was conducted while Mr. Guzmán was on the run from the authorities after an audacious escape from a Mexican prison last year.
The 10,000-word article includes accusations of cooperation between the military and Mr. Guzmán’s Sinaloa cartel, as well as Mr. Guzmán’s acknowledgment of his status as a drug dealer and his thoughts about the ethical implications of his business. Mr. Guzmán, whose escape from prison — his second — made him one of the most wanted fugitives in the world, was caught on Friday, before the article was published.
But after its publication, questions have been raised about the ethics for the magazine in dealing with Mr. Guzmán, a criminal being sought on charges of drug trafficking and murder, and in allowing him to approve what would ultimately be published about him. The Republican presidential candidate Marco Rubio, speaking Sunday on “This Week,” on ABC News, acknowledged Mr. Penn’s “constitutional right” to meet with Mr. Guzmán, but called the interview “grotesque.”
Steve Coll, the dean of the Columbia University Graduate School of Journalism, said he was concerned by the editorial approval offered to Mr. Guzmán. But ultimately, he said, “scoring an exclusive interview with a wanted criminal is legitimate journalism no matter who the reporter is.”
Mr. Wenner said that he did not think it was plausible that the magazine would become embroiled in the legal case against Mr. Guzmán. “They got their man, so what do they need us for?” he said. “There is nothing we can add anymore.”
After Mr. Penn and Mr. Wenner agreed to pursue the article, Mr. Wenner said Rolling Stone strove for secrecy. In early October, he said, he was unable to reach Mr. Penn for a number of days. When Mr. Penn next contacted Mr. Wenner, he said that he had met with Mr. Guzmán, as they had discussed previously. That meeting also included Kate del Castillo, a Mexican actress who once played a drug kingpin on a soap opera. “It was just between me and Sean, for a couple of weeks as he wrote his draft,” Mr. Wenner said.
A lawyer for the magazine, and its managing editor, Jason Fine, were eventually brought in to help with the editing process. Work on the article was completed about two weeks ago, Mr. Wenner said, but because of Rolling Stone’s production cycle, those involved were subjected to an excruciating wait for the next issue, during which time Mr. Guzmán was captured.
The reporting and editing of the article were closely held, in part, to avoid the authorities. “I was worried that I did not want to provide the details that would be responsible for his capture,” Mr. Wenner said. “We were very conscientious on our end and on Sean’s end, keeping it quiet, using a separate protected part of our server for emails.”
Around Thanksgiving, as Mr. Penn negotiated with Mr. Guzmán and his intermediaries to include a video component of the interview, which was eventually sent to him by courier, the magazine was convinced that it would have to resist pressure from the authorities in the United States and Mexico who would want to learn as much as they could about Mr. Guzmán’s whereabouts.
“We made sure we didn’t have any information to give them, other than what we published,” he said. “But we would have done everything that a traditional journalism operation would have done in terms of protecting sources.”
Mr. Wenner said that Mr. Guzmán seemed to have become careless with those he contacted while on the run, and would most likely have been tracked whether or not Mr. Penn wrote an article. In fact, the meeting between Mr. Guzmán and Mr. Penn had been monitored by the authorities, according to a Mexican official with knowledge of the operation. That led to an October raid on Mr. Guzmán’s compound in the state of Durango in which he managed to evade capture but which gave the authorities more intelligence about his movements.
The article was edited by Mr. Wenner and Mr. Fine, with Mr. Fine responsible for the final line editing before publication. Responding to criticisms of the piece’s distinctive writing style, which was mocked on social media, and its discursions into topics including flatulence and technology, Mr. Fine said: “It’s a piece by Sean Penn. Sean Penn has a particular style and point of view, and I’m happy with it.”
Mr. Penn has not commented publicly since the article was published.
Mr. Fine said that he, too, had considered the ethics involved with the article’s publication and the magazine’s arrangement with its subject. If Mr. Guzmán wanted changes, he said, the magazine had the option of not publishing the piece.
There is a long history of journalists interviewing subjects who were either on the run from the authorities or who were considered unsavory for other reasons. Osama bin Laden was interviewed through the late 1990s, after he had declared jihad on the United States (though before the Sept. 11 attacks). In 2013, the former basketball star Dennis Rodman went to North Korea to meet with that country’s repressive dictator, Kim Jong-un, for Vice.
As for giving Mr. Guzmán final approval over the article, Mr. Wenner said: “I don’t think it was a meaningful thing in the first place. We have let people in the past approve their quotes in interviews.”
Mr. Guzmán, he said, did not speak English and seemed to have little interest in editing Mr. Penn’s work. “In this case, it was a small thing to do in exchange for what we got,” Mr. Wenner said.
Still, critics of Rolling Stone remain unconvinced. Andrew Seaman, the chair of the ethics committee for the Society of Professional Journalists, wrote in a blog post that “allowing any source control over a story’s content is inexcusable.”
The practice of pre-approval, he said, “discredits the entire story — whether the subject requests changes or not. The writer, who in this case is an actor and activist, may write the story in a more favorable light and omit unflattering facts in an attempt to not to be rejected.”
Mr. Coll agreed that the offer of preapproval was wrong. But, he said, “It’s hard to judge what Rolling Stone was thinking since apparently the veto wasn’t exercised, freeing the magazine of any dilemma.”
For the magazine, Mr. Wenner said, the interview with El Chapo represented a welcome turn. It was believed to be the first interview Mr. Guzmán had granted in decades.
Last year, Rolling Stone was heavily criticized for a discredited article that alleged a brutal gang rape had taken place at the University of Virginia. After publication, the police, and people close to that situation, questioned the article’s veracity.
A report commissioned by Rolling Stone in the wake of the controversy over the article, and co-authored by Mr. Coll, concluded that the rape article was the result of failures at every stage of the reporting and editing process. The magazine retracted the article and became the subject of lawsuits filed on the matter.
Of Mr. Penn’s article, which was subject to follow-up interviews with eyewitnesses for fact-checking, Mr. Wenner said, “It’s not a vindication but a restatement of how good we are, how strong we are.”