The interview with Sean Penn 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 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 [Jann Wenner, Founder of Rolling Stone Magazine] 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.”

Ethics In Interviewing El ChapoÂ