Interior Minister Miguel Angel Osorio Chong yesterday said the National Security Commission exhausted all legal options for "this criminal to remain in prison" following a court ruling that granted him house arrest.
The 86-year-old drug capo, alias "Don Neto," was convicted for the 1985 murder of US Drug Enforcement Administration agent Enrique "Kiki" Camarena, a crime that strained US-Mexican relations at the time.
Last year, a federal court approved Fonseca Carrillo's request to serve the final years of his 40-year sentence under house arrest for health reasons.
The move would come three years after one of Fonseca's accomplices, veteran drug baron Rafael Caro Quintero, was released by a judge on a legal technicality with 12 years left in his 40-year sentence.
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Caro Quintero's release in 2013 angered the US government, which is seeking his extradition to put him on trial in US court over Camarena's murder.
Caro Quintero, who is in hiding, denied killing the DEA agent in an interview that was published by Mexican magazine Proceso on Sunday. He also rejected allegations that he is back in the drug business.
They are considered the forefathers of Mexico's modern drug cartels.
Camarena's murder was considered a vendetta by the Guadalajara cartel for the DEA agent's investigations that led to the seizure of a massive marijuana field in the northern state of Chihuahua.