MEXICO CITY — During the years that Gen. Salvador Cienfuegos spent as Mexico’s defense secretary, he would sometimes brag about the partnership he helped build with American officials.

“The only thing that I am sure of is that the bilateral, military-to-military and defense-to-defense relationship between Mexico and the United States will continue to strengthen more and more,” Cienfuegos told Craig Deare, a former assistant U.S. defense attache in Mexico and a military historian, before leaving office in late 2018.

Now, Mexican and U.S. officials are left to pick up the pieces after Cienfuegos was arrested in Los Angeles earlier this month on U.S. charges that he had aided a drug cartel during his six years as the country’s top defense official.

The allegations have shocked Mexicans and humiliated the military, one of the country’s most venerated institutions. Some officials worry the backlash could damage cooperation in the fight against narcotics trafficking.

Mexico’s president, Andrés Manuel López Obrador, has suggested that the arrest might have been made “for political or other reasons” and accused the Drug Enforcement Administration of “meddling.”

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Some current and former U.S. officials say that going after Cienfuegos might not have been worth it, considering its potential impact. Mexico’s military often spearheads anti-narcotics operations and benefits from U.S. training, equipment and intelligence.  

“I would argue that maintaining an effective bilateral relationship is more important than the DEA or Department of Justice getting a scalp,” Deare said. “The government of Mexico is well within its rights to be upset that we disregarded their sovereignty, their institutions. In effect, we prioritized the wrong thing.”

Court documents detail how Cienfuegos allegedly used his power to help the H-2 Cartel, tipping the group off to U.S. operations and sparing it from Mexican military operations. Investigators say they obtained thousands of BlackBerry messages that purportedly describe those actions.

Cienfuegos has not yet responded publicly to the charges.

Court documents detail how Cienfuegos allegedly used his power to help the H-2 Cartel, tipping the group off to U.S. operations and sparing it from Mexican military operations. Those actions were allegedly detailed in thousands of BlackBerry messages obtained by investigators.

Most senior U.S. officials apparently did not know the suspicions about Cienfuegos, even as he was being investigated.

Last December, the same office that indicted Cienfuegos, the U.S. attorney’s office for the Eastern District of New York, issued similar charges against Genaro García Luna, Mexico’s public-security minister from 2006 to 2012. He denies the allegations.

Both cases have forced U.S. diplomats to revisit their interactions with Mexican officials.

In February 2018, the U.S. ambassador to Mexico threw a dinner at her home for then secretary of state Rex Tillerson, according to two people who were present. Among the guests was Cienfuegos, who was viewed as helping the military relationship improve in recent years.

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“We had no indication from anyone that including him in the secretary’s schedule would be anything we should be concerned about,” said a senior U.S. official, who spoke on the condition of anonymity to discuss diplomatic information.

 It’s unclear when U.S. agents identified Cienfuegos as a suspect in their investigation of the H-2 cartel, a once-powerful network with a presence along Mexico’s west coast.

Most senior American officials were apparently unaware of the allegations until a grand jury handed up an indictment against him in August 2019. Even then, the indictment was sealed and the information was closely held in Washington. The general had retired the prior year.

U.S. officials say they are still hoping to maintain cooperation with Mexico’s defense establishment. Current and former officials say corruption is common in Mexico, but they are not interpreting Cienfuegos’ indictment as a reflection of systemic failings within Mexico’s military.

“If you never did anything with someone who had rumors against them you couldn’t work with anybody at all,” said Evan Ellis, a professor at the U.S. Army War College, who previously served on the State Department’s Policy Planning staff. “At the same time, you have to be cautious.”

Ellis said U.S. personnel may have heard disparaging rumors about Cienfuegos, but such information often proves spurious. They would have been required to halt cooperation under U.S. law if there had been evidence to support the rumors.

Even when such rumors are substantiated, acting on them sometimes comes at a significant diplomatic cost.

“While justice might be done in individual cases, I don’t see how this helps drug cooperation in the long term, just because it’s going to generate real, if not hostility, at least real suspicion within the Mexican military about what we’re really up to,” said one former senior U.S. official who spoke on the condition of anonymity to discuss a sensitive diplomatic issue.

U.S. prosecutors take a different view. They said in court papers that Cienfuegos “abused” his position to help an “extremely violent Mexican drug trafficking organization” that sent thousands of kilograms of heroin, cocaine, methamphetamines and marijuana to the United States.

López Obrador, who ran on an anti-corruption platform, initially called the allegations against Cienfuegos “regrettable” and pledged to remove any defense officials implicated in the case. He has since seemed to grow more skeptical of the investigation.

His government relies heavily on the military, not only to combat organized crime but to do jobs from building an airport to refurbishing hospitals.

Mexican officials and analysts said that the Mexican military would view Cienfuegos as someone who was willing to work with the U.S. government, only to have it turn on him. Many have been incredulous at the idea that such a prominent official would risk his career to help a second-tier cartel.  

“Show us those operations of complicity if they have the proof,” López Obrador said Monday.

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Another senior Mexican official, speaking on the condition of anonymity, called the indictment “a moral blow to the relationship.”

Mexico’s defense department declined requests for comment.  

Even top officials in López Obrador’s administration were not told about the indictment in advance of Cienfuegos’ arrest, which added to the anger for some.

“This act is so surprising and unilateral, what it will generate is reluctance on the part of the Mexican institutions to work with U.S. agencies. This, in the medium and short term, hurts the U.S.,” said Guillermo Valdés Castellanos, the former head of Mexico’s intelligence agency, the CISEN.

Since 2008, the United States has spent $1.6 billion in equipment and training for Mexican security personnel.

Senior Mexican military officials have been accused of working for cartels in the past. In 1997, the drug enforcement chief, Gen. Jesús Gutiérrez Rebollo, was arrested and later convicted of helping Amado Carrillo Fuentes, the chief of the Juarez cartel.

Those incidents caused U.S. officials to approach their Mexican counterparts warily, often assuming that intelligence could be compromised. But the arrest of a former defense secretary on drug charges was stunning.  

In Mexico, however, many critics have focused on as much on the behavior of U.S. law-enforcement agencies as on Cienfuegos’ actions. Some columnists have alleged that American agents violated Mexican law by conducting surveillance of the former general’s communications. However, there is no evidence so far of that. The United States and other governments have reportedly been able to hack into BlackBerry accounts in recent years, without needing to send agents abroad.

“Nobody pretends that these agencies operate in Mexico in a glass house. But the autonomy with which they operate, behind the backs of their Mexican counterparts, is outrageous,” wrote Héctor Aguilar Camín, a prominent Mexican novelist and historian, in the newspaper Milenio.  

Ryan reported from Washington.

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