The Mexican drug lord is being held in a maximum security prison in New York after he was extradited last month.
El Chapo Guzman escaped twice from prison in Mexico, once in a laundry basket and most recently through a tunnel in his cell.
His lawyers say he has been denied marital visits and is largely kept in solitary confinement.
The claims arose at a federal court in Brooklyn at a hearing for El Chapo Guzman, who has pleaded not guilty to charges that he ran the world’s largest drug-trafficking organization during a decades-long career.
El Chapo Guzman faces life in prison if convicted.
His wife Emma Coronel, a 27-year-old former beauty queen and mother of his twins, flew from Mexico to attend the hearing.
El Chapo Guzman’s lawyers said it was first time Emma Coronel had seen her husband since his surprise extradition two weeks ago.
The 59-year-old is reportedly on 23-hour lockdown in a special unit of the Manhattan Correctional Center.
Michelle Gelernt, one of El Chapo Guzman’s court-appointed lawyers, said: “We understand the need for security but we think it has gone above and beyond.”
District Judge Brian Cogan pointed out that the “history of the defendant is somewhat unusual” – a reference to his past escapes – and said the Federal Bureau of Prisons should decide what conditions El Chapo Guzman faced and who he could see.
His Sinaloa cartel allegedly smuggled hundreds of tonnes of cocaine, heroin, marijuana and methamphetamines to the US while waging war with other gangs.
The cartel is accused of carrying out thousands of murders and kidnappings, and bribing officials.
El Chapo Guzman is believed to have amassed a billion-dollar fortune through the drugs trade.
Mexican President Enrique Pena Nieto had initially resisted extraditing the drug lord to the US, insisting that he should face justice at home.
However, after El Chapo Guzman was recaptured in January 2016, President Pena Nieto changed his mind on extradition and ordered officials to speed up the process.
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