The comment prompted a protest from Mexico, which accused the pontiff of stigmatising the country and being dismissive of its efforts to dismantle cartels thought to control most of the cocaine entering the United States.
A Vatican spokesman said Wednesday that Secretary of State Pietro Parolin had sent a letter to the Mexican ambassador to the Holy See to smooth over the row.
"The Secretary of State has clarified that when he used the expression 'avoid Mexicanisation' the pope had absolutely no intention of hurting the feelings of the Mexican people, whom he loves very much, nor of giving the impression that he does not appreciate the commitment of the Mexican government in the fight against narco-trafficking," the spokesman said.
"The letter underlines that obviously the pope's intention was simply to highlight the gravity of the phenomenon of narco-trafficking that afflicts Mexico and other Latin American countries."
The pope's controversial comment was made in an email he wrote to an Argentinian friend, Gustavo Vera, who heads an NGO called "Alameda" which is involved in combating organised crime and human trafficking.
"I hope we (in Argentina) can avoid Mexicanisation. I have spoken with Mexican bishops and it is a terrifying reality," Francis wrote in a message which Vera made public.
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