Javier Duarte had been staying at the four-star hotel under a false name for at least two days. In June, the opposition National Action Party won a hotly contested race to succeed Duarte in a contest widely seen as a repudiation of rampant corruption and a stinging defeat for the PRI.
Mexico filed its extradition request later that night.
Speaking previous year after he was accused of having links to phantom businesses that had successfully bid for state contracts, Duarte denied the accusations against him. "I understand that he will accept his extradition", said Duarte's lawyer Rodrigo Sandoval.
Mexican authorities issued an arrested warrant against Duarte in October for his alleged responsibility in organized crime and embezzlement.
"For many Mexicans, Duarte came to symbolise the worst aspects of the political class here: corruption, incompetence and, until his capture, impunity", Al Jazeera's John Holman, reporting from Mexico City, said.
Elías Beltran stated that two people provided Javier Duarte with the logistics for taking refuge in Guatemala.
Javier Duarte, who until past year governed Veracruz state for President Enrique Pena Nieto's Institutional Revolutionary Party (PRI), became a symbol of corruption in Mexico and his case is highly politicized with elections looming.
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"I have no comment, thank you", the former Institutional Revolutionary Party, or PRI, governor said to a question from The Associated Press as he entered the prison.
The Mexican government has found millions of dollars purportedly linked to Duarte, frozen more than 100 bank accounts and also seized property and businesses tied to the former governor.
Another former governor, César Duarte of Chihuahua state, no relation to Javier Duarte, remains at large. The governors have in part been shielded by laws that make it hard for federal authorities to audit state governments and prosecute wrongdoing by state officials, experts say.
Duarte, a fugitive from justice suspected of embezzling hundreds of millions of dollars, will be processed for extradition to Mexico. A reward of 15 million pesos ($730,000) had been offered for his capture.
Drug cartels warred for territory and thousands of people were killed or disappeared into clandestine graves in cases that mostly remain unsolved.
Duarte was a PRI stalwart for years until he was expelled from the PRI in October.
During his roughly six years in office, Duarte's Gulf Coast state also earned the inglorious distinction of becoming "one of the world's most lethal regions for the press", according to the Committee to Protect Journalists.