Mexico’s former defence minister will return to his home country after a judge granted a request by US prosecutors to drop drug trafficking and money laundering charges against him, citing “sensitive and important foreign policy considerations”.

The US justice department’s decision to abandon the case against Salvador Cienfuegos, a 72-year-old retired four-star general, came barely a month after his arrest at a Los Angeles airport, which had threatened to upend security co-operation between the two countries.

In a court filing on Tuesday, federal prosecutors in Brooklyn insisted that “the evidence in this case is strong” but that Mexico’s investigation and potential prosecution should be allowed to proceed “in the first instance”.

“The United States has determined that sensitive and important foreign policy considerations outweigh the government’s interest in pursuing the prosecution of the defendant,” prosecutors said.

During a court hearing over the government’s request, Seth DuCharme, the acting US attorney in Brooklyn, acknowledged that the decision to drop the case had been made at the highest level of the US justice department — William Barr, the attorney-general appointed by President Donald Trump.

Judge Carol Amon ultimately granted the request on Wednesday, saying: “Although these are very serious charges against a very significant figure, and the old adage ‘a bird in the hand’ comes to mind, I have no reason to doubt the sincerity of the government’s decision.”

Nor did she doubt the US government’s determination that Mexico “sincerely” wished to pursue the case, she added.

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The general, who was due to be flown back to Mexico by US marshals, had pleaded not guilty to the four charges of drug trafficking and money laundering he had faced in New York. Minister from 2012-18, Gen Cienfuegos was a key player in Mexico’s fight against drug cartels and mounting violence.

US evidence about his alleged complicity with the H2 drug cartel included thousands of intercepted BlackBerry communications.

Andrés Manuel López Obrador, Mexico’s president, thanked the Trump administration for moving to drop the case following a formal protest by Mexico that it had been kept in the dark about the investigation into the general and his arrest. He promised there would be no impunity and that he had given “nothing in exchange”.

“I want to thank the US government . . . they listened and rectified,” the president told his morning news conference shortly before the court hearing. “We are not a colony.”

He added: “There is no impunity for any one and we will not permit, in any case, for crimes to be fabricated.”

Mr López Obrador’s refusal so far to recognise Joe Biden as winner of the US presidential election until legal appeals have ended sparked speculation that Mr Trump was dropping the case as a favour to Mexico, which the Mexican leader denied.

Any decision whether to arrest Gen Cienfuegos to face charges in Mexico would be taken by Mexico’s attorney-general’s office, Mr López Obrador said.

The president, who said he was spearheading a crusade to eradicate corruption and impunity, has made the military a key ally but denied he had bent the rules to secure the general’s release after outrage from the armed forces. “We don’t accept pressure from anyone,” he said.

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However, one senior former military official said the armed forces had been irate at the arrest and had made their position clear to Mr López Obrador: “If you don’t help us, we won’t help you.”

Marcelo Ebrard, Mexico’s foreign minister, underscored that future co-operation on combating drug trafficking and security issues had been at stake. The US and Mexico are signatories to a 1992 security co-operation treaty.

“If we are going to maintain bilateral co-operation, you have to respect Mexico,” he told the news conference. He said he had told Mr Barr: “You can’t have close co-operation with Mexico and at the same time do this, you have to choose.”

Mexico earlier this month received nearly 750 pages of documentation in the case and other evidence. It was not immediately clear whether it would be admissible in a Mexican court.

Mr Ebrard insisted the allegations would not simply be dropped. “If you’re planning to shelve it [the case], you don’t ask for all the evidence,” he said.

Few, however, expect to see the general behind bars in his home country.

“The idea that he could be publicly tried is ludicrous — he knows exactly where all the bodies are buried,” said Benjamin Smith, a professor at University of Warwick and an expert on the Mexican drug trade.

“Diplomatic pressures and sovereignty considerations that sound very outdated, very nationalistic, matter more than protecting citizens or bringing people to justice,” said Gema Kloppe-Santamaría, a professor at the Loyola University Chicago.

“This sets a very bad precedent, it sends a signal justice will be sacrificed . . . to behind-doors dealing.”

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Via Financial Times