The court documents were unsealed following a request by Vice News and the New York Times.
One of Guzman's lawyers called the accusations "extremely salacious" and questioned the timing of the government filing.
A jury at Guzman's drug-trafficking trial in NY is due to begin deliberating on Monday.
El Chapo's lawyers called the accusations "extremely salacious" and questioned the timing of the government filing, which comes as a jury is about to start deliberating in his United States drug-trafficking case. He is accused of leading the Sinaloa drug cartel, largely considered to be one of the most powerful and ruthless criminal organizations in existence.
The defense claims his role has been exaggerated by cooperators who are seeking leniency in their own cases.
United States district judge Brian Cogan had ordered prosecutors to review the material - which had been sealed because it was deemed unrelated to the drug charges.
Through them, jurors heard how the Sinaloa cartel gained power amid the shifting allegiances of the Mexican drug trade in the 1990s, eventually coming to control nearly the entire Pacific coast of Mexico.
For 5,000 dollars (£3,800), the girl of El Chapo's choice would be sent to a secluded Sinaloa ranch, Cifuentes said, according to the papers.
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The former Sinaloa cartel leader, 61, would allegedly sometimes drug the girls with "a powdery substance" with Cifuentes' help before raping them.
The documents had been sealed because prosecutors had convinced the court that the allegations were "irrelevant" to the drug conspiracy charges against El Chapo, who already is facing 10 federal counts that can find him spending the rest of his life in prison.
Guzman "called the youngest of the girls his "vitamins" because he believed that sexual activity with young girls gave him "life", Cifuentes added.
The document said other government witnesses corroborated the allegations.
Cifuentes said he also had sex with the girls, but did not drug them.
The cooperator told the government that he saw Guzman "consulting with a witch doctor from whom he obtained sake oils", the papers said.
The 11-week trial, which featured testimony from more than 50 witnesses, offered the public an unprecedented look into the inner workings of the cartel, named after the state in northwest Mexico where Guzman was born in a poor mountain village.
El Chapo was extradited from Mexico to the United States in early 2017; the drug lord had often escaped from custody.