A former police chief in Honduras was charged Thursday in federal court in New York with helping to ship tons of cocaine into the United States at the behest of the Honduran president and his brother.

Juan Carlos Bonilla Valladares, widely known as The Tiger, was named police chief in 2012 as part of a sweeping campaign to clean up a corrupt department, despite having previously faced murder charges himself.

Federal prosecutors in New York accused Mr. Bonilla of using his position to help powerful politicians involved in drug trafficking — namely, the former congressman Juan Antonio Hernández Alvarado, widely known as Tony, and his brother, the president, Juan Orlando Hernández Alvarado.

The president’s brother was convicted of drug trafficking in New York last year and is expected to be sentenced in June.