The 60-year-old, accused of running one of the world's biggest drug empires and who escaped twice from prison in Mexico, has been held in solitary confinement in New York since being extradited on January 19.
Federal Judge Brian Cogan ruled that Guzman, one of the world's most notorious criminals, could send written messages to his wife -- provided they were pre-screened by multiple federal agencies -- but denied him family visits and phone calls.
The 18-page ruling follows complaints from Guzman's lawyers about the conditions of his pre-trial detention. The judge similarly allowed his defenders' pre-cleared investigator to visit without an attorney present.
But Cogan refused a request for Amnesty International to visit on the grounds that there was "absolutely no reason."
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The London-based rights groups in March asked to speak with Guzman, expressing concern that the conditions of his detention "appear to be unnecessarily harsh and to breach international standards for human treatment."
Cogan also flatly denied Guzman's request to have his "special administrative measures" lifted in full or for him to be moved out of solitary confinement.
"The court would be hard pressed," he wrote "not to acknowledge" that Guzman's second jail break in Mexico "was accomplished under 24-hour video surveillance in solitary confinement."
The decision came one day before Guzman is due to appear in court for another pre-trial hearing. His wife is also expected to attend.
Cogan denied Guzman visits from anyone other than his lawyers or permission to communicate with potential witnesses.
Cogan's ruling revealed that Guzman is visited by his lawyers almost every day at the Metropolitan Correctional Center in Manhattan, for an average of four to five hours in a windowed visitor room.
But Cogan declined to intervene on complaints over the size of Guzman's cell, his window, whether he could hear "phantom music" or television programming during his daily hour of exercise.
In March, the defense complained Guzman's health was deteriorating in custody, and claimed that he experienced "auditory hallucinations" and heard unexplained music.
On January 20 Guzman pleaded not guilty to a raft of firearms, drug trafficking and conspiracy charges at an initial hearing in New York.