A Brooklyn federal judge on Friday refused to lift tough security conditions on Joaquin “El Chapo” Guzman Loera that have kept the alleged drug lord from seeing his wife or Mexican lawyer in jail, and prohibit his U.S. lawyers from even giving him a glass of water.

“It is an unusual case,” U.S. District Judge Brian Cogan said, referencing secret letters he got from the government about the special security risks of Guzman, who twice escaped Mexican jails — once through a mile-long tunnel.

“Based on what I know there are grounds for taking extra security precautions,” Cogan said.

Guzman’s wife, statuesque ex-beauty queen Emma Coronel, sat in the first row wearing a yellow scarf and the gnomish alleged kingpin — whose nickname means “Shorty” — peered at her and smiled. But his public defenders said he had been barred from seeing or speaking to her since his Jan. 20 extradition to the United States.

They also complained that he hadn’t been allowed phone calls or visits with his Mexican lawyer, and was locked in solitary 23 hours a day. When he talks to his U.S. lawyers by phone, they said, their office has to be cleared of anyone but two approved paralegals, and when they visit they can’t even offer him a sip of water.

“To the sort of glib remarks about his prior experiences . . . in the Mexican prisons, I don’t think there’s any thought that if I have the guards give him a glass of water during a three-hour meeting that somehow that’s going to effectuate his escape,” complained defense lawyer Michelle Gelernt.

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Coronel did not speak, but stood with Gelernt as she spoke to reporters about the restrictive conditions. “This was so far the only way she has been able to see him,” the lawyer said.

Guzman, 59, is accused of cocaine trafficking and violence on a massive scale through his Sinaloa cartel, raking in $14 billion and moving tons of drugs into the United States. He was indicted in Brooklyn and six other jurisdictions, and has been held in a federal jail in lower Manhattan since his extradition.

Cogan wanted to hold the hearing via video hookup with Guzman in the jail, but he objected, and photographers Friday morning recorded a heavily guarded caravan bringing him to Brooklyn.

Although prison officials haven’t specified the reasons for the tight visiting restrictions, the government in court papers has said that in addition to his escapes, Guzman continued to run his drug organization from Mexican jails. Before his extradition, Coronel visited him dozens of times and spearheaded a human rights campaign on his behalf, according to published accounts.

During Friday’s hearing, Guzman’s lawyers signaled that they are likely to challenge his extradition because Mexico approved his removal to face charges in Texas and California, and then he was taken to Brooklyn. But prosecutors said the Mexican government later signed a waiver approving his transfer to Brooklyn.

Cogan set the next hearing in the case for May.