But the papers were opened after lawyers for the New York Times and Vice News filed an application to make them public.
They heard how Guzman made a name for himself in the 1980s as "El Rapido", the speedy one, by building cross-border tunnels that allowed him to move cocaine from Mexico into the U.S. faster than anyone else.
On Saturday, 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.
The jury has heard months of testimony about Guzman's rise to power as the head of the Sinaloa cartel.
The defense claims Guzman's role has been exaggerated by cooperating witnesses who are seeking leniency in their own cases.
The jury begins deliberation on Monday after hearing from a total of 57 witnesses: 56 presented by the prosecution and one called by Guzman's defense team.
The infamous drugs lord "denies the allegations, which lack any corroboration and were deemed too prejudicial and unreliable to be admitted at trial", Eduardo Balarezo said in a statement.
"This trial gave the American public tremendous insight into how these powerful drug trafficking cartels operate", Mike Vigil, former chief of global operations for the Drug Enforcement Administration, said, according to CNN.
He alleges that an associate of Guzman named "Comradre Maria" would send him pictures of girls, and for $5,000 the girl Guzman selected would be sent to his ranch.
"Guzman directed Cifuentes to put a "powdery substance" into the girls" drinks before sex, said Cifuentes.
He could be sentenced to life in prison if found guilty on the top charge of engaging in a continuing criminal enterprise.
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 U.S. drug-trafficking case.
The document says other co-operating witnesses have backed up the claims about El Chapo's interactions with underage girls.
The cooperator told the government that he saw Guzman "consulting with a witch doctor from whom he obtained sake oils", the papers said.
Guzman, 61, faces 10 federal counts, including engaging in a continuing criminal enterprise, conspiracy to launder narcotics proceeds, worldwide distribution of cocaine, heroin, marijuana and other drugs, and use of firearms.
The new and disturbing details were made during Guzman's trial at the U.S. Federal Court in Brooklyn, New York on Friday.