The charges against General Salvador Cienfuegos Zepeda were dropped this week, along with reports that the charges were dropped because the Mexican government threatened the agency out.
"There was never a threat and there was never even concern on DEA's part that that would happen," a senior DEA official told ABC News. "The Mexican government has an interest in having DEA there. They don't want the Mexican cartels there either. It hurts their economy … we were not concerned at all that our agents would be thrown out of Mexico that's not going to happen."
"This was all about maintaining our, close, close relationship and evidence sharing and working with them very closely," the official said.
Mexico has extradited more than 50 defendants to the U.S. in the past year, the official added.
Andrés Manuel López Obrador, the president of Mexico, also denied there was any threat to expel DEA agents from Mexico.
"Now they are saying we threatened to expel U.S. agents from Mexico, we didn't threaten anyone," he said. "The only thing we did was to express our disagreement through a diplomatic note and they understood us well. Now, the Mexican attorney general's office will be in charge of the investigation."
Former DEA Deputy Director Jack Reilly told ABC News this was "baffling."
"I don't see how this could have happened without all the, you know, bases being touched prior to indicting right it seems like in a typical case with a high profile defendant like that, especially somebody who has entanglements with a foreign government that all that stuff would be ironed out before the charge was made," he said, adding that it seems as though there was an "overpowering influence coming from Mexico that had rang the bell in Washington."
Media outlets reported that the Mexican government threatened to throw the agency out of the country due to these charges.
In early October, the Justice Department charged Cienfuegos with allegedly working with drug cartels.
"The defendant abused that public position to help the H-2 Cartel, an extremely violent Mexican drug trafficking organization, traffic thousands of kilograms of cocaine, heroin, methamphetamine and marijuana into the United States, including New York City," according to a detention memo submitted to the judge.
The H-2 Cartel routinely engaged in wholesale violence, including torture and murder, prosecutors said.
In court on Wednesday, Acting U.S. Attorney for the Eastern District of New York Seth DuCharme confirmed Attorney General William Barr himself made the decision to drop the case.
On Thursday, the Mexican attorney general's office issued a statement saying Cienfuegos arrived back in Mexico aboard a U.S. government jet.
At the airport, he was formally notified of an investigation being conducted using information shared by American authorities, but he was not detained or charged and was allowed to go home. The statement says Cienfuegos agreed to appear whenever questioned as part of the investigation.