The US made the unusual decision to drop drug-trafficking charges against former Mexican Secretary of National Defense Salvador Cienfuegos Zepeda because it determined that maintaining its relationship with Mexico is more important than pursuing the prosecution, a federal prosecutor said Wednesday.

“Here there was a balancing frankly of interest between the department’s interest in pursuing this particular prosecution against the interest of the United States in foreign relations, and in particular with the United States’ relationship with Mexico and cooperative law enforcement efforts that go, that touch upon this case,” Acting US Attorney Seth DuCharme said in Brooklyn federal court.

“The United States determined that the broader interest in maintaining that relationship in a cooperative way outweighs the department’s interest in … pursuing this particular case.”

US District Judge Carol Bagley Amon agreed to grant the dismissal. Cienfuegos, who was present in court, will now be turned over to Mexican authorities for possible prosecution.

“This motion to seek dismissal was made at the highest level of government: the Justice Department, that is the attorney general of the United States,” said Amon.

“Although these are very serious charges against a very significant figure and the old adage ‘A bird in the hand’ comes to mind, still I have no reason to doubt the sincerity of the government’s position,” she said before granting the dismissal of the indictment.

The surprise move came just weeks after Cienfuegos, 72, was arrested in Los Angeles for allegedly taking bribes during his time in office to help leaders of the violent H-2 cartel move cocaine, heroin, methamphetamine and marijuana into the US.

Cienfuegos — nicknamed “El Padrino,” or “the Godfather” — led the country’s army for six years starting in 2012 under former President Enrique Peña Nieto.

Brooklyn prosecutors said he was reporting directly to the president — all while secretly communicating with the cartel’s senior members and helping them flood the US market with drugs.

In 2014, Cienfuegos endured a major scandal after soldiers under his command killed 22 suspects at a grain warehouse — at least eight of whom were executed after they surrendered, according to a human rights investigation.

Cienfuegos’ arrest had come as a shock to Mexican government officials and the current president of the country, Andrés Manuel López Obrador, who were angered over the lack of communication, the New York Times reported.

Prosecutors can seek to dismiss a case for reasons of national security and foreign policy, DuCharme wrote in seeking to do just that.

“Situations may arise where substantial reasons of national security, foreign policy or the like may require the Department to abandon an investigation, forego litigation, or seek dismissal of a case,” the motion states.

Attorney General William Barr and his Mexican counterpart, Alejandro Gertz Manero, released a joint statement Tuesday announcing the move.

“In recognition of the strong law enforcement partnership between Mexico and the United States, and in the interests of demonstrating our united front against all forms of criminality, the US Department of Justice has made the decision to seek dismissal of the US criminal charges against former Secretary Cienfuegos, so that he may be investigated and, if appropriate, charged, under Mexican law,” the statement read.

Barr said the US had turned over its evidence against Cienfuegos to Mexican authorities.