He was taken to a prison near Ciudad Juarez, across the border from El Paso in Texas, as part of a normal rotation of prisoners for security reasons, officials said.
The head of the Sinaloa drug cartel, El Chapo Guzman, also known as Shorty, was re-captured in January, six months after he escaped from prison.
Joaquin Guzman is wanted in the US on charges of smuggling drugs into the country.
His transfer to Ciudad Juarez was not a precursor to extradition, Mexican officials told Reuters.
According to Mexico’s National Security Commission, the move was in line with security protocols, and it had rotated more than 7,400 inmates as part of new security strategy.
The authorities said that El Chapo Guzman was moved to a new prison “because of works taking place to reinforce security” in Altiplano – his old prison near Mexico City.
Analysts suggested the move was to prevent him escaping during the works.
El Chapo Guzman, who was named Public Enemy Number One by the Chicago Crime Commission in 2013, has been indicted by at least seven US federal district courts.
According to Mexican officials, the process to extradite him to the US could take at least a year.
In March, El Chapo Guzman asked to be extradited rapidly so he could receive better treatment in prison.
His lawyer said El Chapo Guzman had asked him to stop fighting his extradition because guards at his prison would not let him sleep.
El Chapo Guzman was captured in January and returned to the Altiplano maximum security jail near Mexico City after six months on the run.
He had escaped from Altiplano in July through a one mile-long tunnel under the floor of his shower stall in his cell.
Leaked security footage of El Chapo Guzman’s prison break showed how guards failed to detect his escape until more than 20 minutes after it had happened, despite the sound of loud banging coming from his cell.
Mexican marines arrested him in the western state of Sinaloa after he fled a safe house through a storm drain.
Altiplano director and a number of guards were arrested in connection with El Chapo Guzman’s escape.
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