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4 year oldGen Salvador Cienfuegos Zepeda was detained on Thursday, Mexico's foreign minister Marcelo Ebrard tweeted.
Gen Cienfuegos was arrested on a US Drug Enforcement Administration (DEA) warrant, the Mexican government confirmed for the BBC.
Mexican President Andrés Manuel López Obrador said on Friday the general had been accused of drug trafficking.
"Hopefully this serves to illustrate that the main problem in Mexico is corruption," the president said, before praising Gen Cienfuegos' successor at the head of the army and his counterpart in the navy.
President López Obrador, who was elected on an anti-corruption platform in 2018, has accused his predecessors of running a "narco-government" that allowed corruption.
He is seeking to lift the immunity of former leaders from prosecution.
Gen Cienfuegos, 72, served as minister from 2012 to 2018, under President Enrique Peña Nieto.
His role as the most senior member of the armed forces meant he played a key role in Mexico's war on drugs.
But there were accusations of complicity between the state and the country's powerful drug cartels throughout Mr Peña Nieto's presidency, reports BBC Mexico correspondent Will Grant.
Earlier this year, one of the former president's closest advisers was extradited to Mexico from Spain on corruption charges.
Emilio Lozoya, the former boss of Mexican state oil company Pemex, is accused of taking $10m (£8m) in bribes from a Brazilian construction firm that has admitted paying off Latin American politicians. He has denied any wrongdoing.
Mr Peña Nieto has not been implicated.
Gen Cienfuegos is not the first former Mexican minister to have been arrested in the US.
Last December, former Security Minister Genaro García Luna was charged with taking bribes from a drugs cartel.
Mr García Luna, who was Mexico's top security chief from 2006 to 2012, is currently on trial in New York, accused of allowing the Sinaloa cartel of "El Chapo" Guzman to operate in Mexico in exchange for millions of dollars.
He denies all the charges against him.
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