Gen Salvador Cienfuegos Zepeda, 72, acted on behalf of the H-2 cartel while he was defence secretary from 2012 to 2018 under former president Enrique Pena Nieto, authorities said.
Thousands of intercepted Blackberry messages show the general ensured military operations were not conducted against the cartel and that operations were initiated against rivals, according to prosecutors.
Cienfuegos allegedly introduced cartel leaders to other corrupt Mexican officials.
Cienfuegos is accused of alerting cartel leaders to a US law enforcement investigation into its operations and the use of cooperating witnesses and informants, which resulted in the murder of a member of the cartel that leaders incorrectly believed was assisting US law enforcement authorities.
Intercepted communications between Cienfuegos and a senior cartel leader discussed the general’s historical assistance to another drug trafficking organisation, as well as communications in which the defendant is identified by name, title and photograph as the Mexican government official assisting the H-2 Cartel.
Cienfuegos was indicted by a grand jury in the Eastern District of New York on August 14, 2019.
Cienfuegos was scheduled to make an initial appearance later on Friday in federal court in Los Angeles, Foreign Minister Marcelo Ebrard said. His lawyer was to traveling LA from Mexico.
Cienfuegos was expected to be transferred to New York, where his case is being handled.
The defence secretary post positioned Cienfuegos as a critical figure in efforts by Mexico and its allies to combat drug trafficking.
He was arrested on Thursday upon arrival at Los Angeles International Airport. A senior Mexican official, who spoke on the condition of anonymity because he was not authorised to give details of the case, said Cienfuegos was arrested with family members who were released and he was taken to the Metropolitan Detention Centre.
Cienfuegos is the highest-ranking former Cabinet official arrested since top Mexican security official Genaro Garcia Luna was taken into custody in Texas in 2019.
Garcia Luna, who served under former president Felipe Calderon, has pleaded not guilty to drug trafficking charges.
The arrest of Cienfuegos is a tough blow for Mexico, where the army and navy are some of the few remaining respected public institutions.
Current President Andres Manuel Lopez Obrador has vowed to go after corruption and lawbreaking under past administrations, but he has relied more heavily on the army — and given it more tasks, ranging from building infrastructure projects to distributing medical supplies — than any other president in recent history.
