He had been on the run for six months since a daring jailbreak in July.
Appeal processThe US has filed a request for Guzman to be extradited to face charges of smuggling vast amounts of drugs into the country.
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.
But Mr Merino said that Guzman could not be extradited to the US straight away.
Speaking on Mexican radio, he explained that Interpol officers went to Altiplano jail on Sunday and served Guzman with two arrest warrants for his extradition.
He said that Guzman’s lawyer could lodge appeals against the order and that the process could be delayed considerably depending on how vehemently they fought his extradition.
Juan Pablo Badillo, one of Guzman’s lawyers, said he would take his appeal all the way to Mexico’s highest court.
Deadly raidGuzman was arrested on Friday in Los Mochis, a seaside town in his home state of Sinaloa, in north-western Mexico.
Five of Guzman’s men were killed in the operation.
He was taken to Altiplano jail, from which he escaped in July through a 1.5km-long (one mile) tunnel.
Mexico’s national security commissioner said the jail “fully meets international [security]protocols” and that improvements had been made since Guzman’s escape.
He also said that a “rigorous surveillance scheme” had been put in place to monitor the access of prison staff and visitors.
Leaked security footage of 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.
The prison director and a number of guards were arrested in connection with his escape.
Probe into Penn roleMexico is also considering whether to investigate Hollywood actor Sean Penn, who interviewed Guzman soon after his jailbreak.
Unnamed Mexican officials have said Penn’s secret meeting helped lead them to the fugitive.
In the Rolling Stone article, the result of a seven-hour meeting, Penn and Guzman discuss various topics, including drug trafficking.
Penn said the meeting was set up by Mexican actress Kate del Castillo.
The actress was approached by Guzman’s lawyers after publishing an open letter to Guzman in which she called on him to “traffic in love” instead of in drugs,
Mexican prosecutors said Guzman wanted her to produce a film about his life.
Del Castillo has not made any public comments since the publication of the Rolling Stone article.
Guzman timelineFebruary 2014: Recapture after 13 years on the run following “laundry basket” escape from Puente Grande maximum security prison
July 2015: Escape via tunnel from Altiplano prison
2 October 2015: Interviewed by US actor Sean Penn in Durango state jungle hideout and then by phone and video
17 October: Mexican officials announce narrow escape as police try to recapture him in neighbouring Sinaloa state
January 2016: Recaptured in Los Mochis, Sinaloa state