Ever since they took the case last year, lawyers for Joaquín Guzmán Loera, the Mexican drug lord known as El Chapo, have mounted a largely procedural defense. In a series of motions about their client’s harsh terms of confinement and the daunting challenge they face in poring through the evidence against him, the lawyers have argued that Mr. Guzmán’s rights are in jeopardy and there is little chance that he will get a fair trial.

But at a court hearing on Tuesday, the lawyers offered their first hint of an affirmative defense of Mr. Guzmán, saying that evidence exists that he may not be what federal prosecutors have claimed he is for months: the top man in Mexico’s Sinaloa drug cartel. Their proof for this assertion came from an unusual source — the government itself — and the lawyers used it to suggest that Mr. Guzmán might not have been the cartel’s leader, but merely “a lieutenant” who took orders from someone else.

From the moment last year that Mr. Guzmán was brought from Mexico to stand trial in New York, the United States attorney’s office in Brooklyn has insisted that until his arrest, he was the world’s biggest drug dealer, a violent kingpin who personally ordered the deaths of thousands during his decades-long reign atop the cartel in Sinaloa. But in a sealed letter sent three weeks ago to Mr. Guzmán’s lawyers, prosecutors acknowledged that over the years, a handful of confidential informants had contradicted that account, telling them that, despite his reputation, Mr. Guzmán may not have been in charge of his own organization.

Prosecutors dismissed this evidence in court on Tuesday as second or even thirdhand, adding that it was mired in “layers of hearsay.” But they were obliged to turn it over to Mr. Guzmán’s lawyers under what is known as the Brady rule, a practice that requires the disclosure of information that could be favorable to a defendant.