Lawyers for Mexican drug kingpin Joaquin "El Chapo" Guzman have complained that he was being subjected to excessive conditions of confinement in a federal jail and that his wife was not being allowed to visit him.

The arguments came in federal court in Brooklyn at a hearing for Guzman, who has pleaded not guilty to charges that he ran the world's largest drug-trafficking organisation during a decades-long career. He faces life in prison if convicted.

Guzman's wife, Emma Coronel, flew from Mexico to attend the hearing, his second appearance in a US court. His lawyers said the hearing was the first time Coronel had seen Guzman since his surprise extradition two weeks ago.

Guzman, 59, who has escaped two maximum-security jails in Mexico, is on 23-hour lockdown in a special unit in the federal jail in Manhattan, according to his lawyers, and has been prevented from seeing Coronel and his Mexican attorney.

"We understand the need for security but we think it has gone above and beyond," said Michelle Gelernt, one of Guzman's court-appointed lawyers.

US District Judge Brian Cogan said he would defer to the Federal Bureau of Prisons to determine what conditions were set and who Guzman could see, saying the "history of the defendant is somewhat unusual."

"Based on what I know of this case, there are grounds for taking additional security measures," Cogan said.

'El Chapo' Guzman's wife Emma Coronel (left) has not been allowed to visit her husband. Photo: Reuters/Brendan McDermid

Following the hearing, Coronel, 27, a former beauty queen, stood by Guzman's attorneys as they complained to reporters about jail restrictions.

Michael Schneider, another of his lawyers, said prosecutors have questioned Guzman's financial eligibility for court-appointed counsel, given what they said was his position as the billionaire leader of the Sinaloa cartel.

Schneider called that position "ridiculous" given that prosecutors were simultaneously supporting strict jail conditions that have blocked Guzman from talking to his family, who could help him retain counsel.

Guzman's cartel allegedly smuggled hundreds of tonnes of cocaine, heroin, marijuana and methamphetamines to the United States while waging war with other cartels, carrying out thousands of murders and kidnappings and bribing officials.

At the hearing, Guzman's lawyers also sought documents related to his extradition. Gelernt told reporters the defence is concerned about the legality of Guzman's extradition to face the Brooklyn case, which not the subject of the initial US request to Mexico.

Prosecutors have said that after Guzman was extradited to face indictments in California and Texas, the Mexican government approved a US request to prosecute him in New York.