Guzman’s transfer, conducted under a large military security presence, was determined “solely by security protocols as part of a rotation of prisoners” that normally takes place, the official said, speaking on condition of anonymity.
Guzman, who was arrested last January and held in a maximum security prison in Altiplano, 90 kilometers (55 miles) from the capital Mexico City, arrived at the airport in Ciudad Juarez at dawn, heavily guarded by some 150 federal police officers who had arrived earlier in three planes.
A helicopter transferred Guzman from the airport to a prison in the south of the city.
Although not classified as a maximum security prison, it has a section for highly dangerous prisoners that is “one of the safest,” the source said.
Military soldiers guard the prison, and the road leading to the facility is under especially heavy protection, Mexican media reported.
The former leader of the Sinaloa drug cartel — one of Mexico’s most powerful — Guzman staged a spectacular jailbreak in July 2015, when he escaped through a hole in his jail cell’s shower that led to a 1.5-kilometer (1-mile) tunnel leading outside.
He was captured in January after months on the run in a colorful episode involving a Mexican soap opera actress and US film star Sean Penn, who met with the drug boss in hiding.
Considered one of the world’s most powerful drug bosses, Guzman has twice escaped from maximum-security prisons.
In March, a court overturned his appeal seeking to block the government’s request for an extradition warrant, dealing a blow to his battle against efforts to extradite him to the United States.
He faces two extradition demands by courts in California and Texas, for homicide and drug trafficking.
Mexican authorities have said the extradition process may take a year or more.