NEW YORK — U.S. prosecutors say the president of Honduras took a $25,000 bribe years ago from an alleged cocaine trafficker now in federal custody, a startling development that could complicate relations between the two countries.

President Juan Orlando Hernández was identified in court papers following the arrest in recent days of Geovanny Fuentes Ramírez, whom U.S. authorities have labeled a major narcotics supplier. In the documents, U.S. officials linked Hernández to a cocaine and weapons case and said the bribe was made in 2013, the year Hernández was first elected. He has not been charged.

The Associated Press was first to report the allegations Tuesday. The Honduran president’s office rejected the claim in a brief statement posted on Twitter.

“The story that President @JuanOrlandoH supposedly accepted drug money from Geovanny Daniel Fuentes Ramirez, or provided protection or coordinated with narcotraffickers, is 100% false and appears to be based on lies from confessed criminals who are seeking vengeance or to reduce their sentences,” the tweet says.

A spokesman for the U.S. attorney’s office in Manhattan declined to comment.

U.S. officials alleged in the court papers that Hernández accepted  the  $25,000  bribe “on the understanding that [he] would facilitate protection for [Fuentes Ramírez] from law enforcement scrutiny.” They also alleged that Hernández agreed to put Honduran armed forces to work providing security for him.

Fuentes Ramírez was arrested at Miami International Airport on Sunday. He is in custody at a federal jail in Miami and is expected to be extradited to face his charges in New York.

Fuentes Ramírez “paved the way for unimpeded shipment of multi-ton loads of cocaine by bribing police and a high-ranking Honduran politician, and reporting directly to Tony Hernandez, another co-conspirator in the scheme and himself a former Honduran congressman,” U.S. Attorney Geoffrey Berman said in a statement Tuesday.

Tony Hernández is the Honduran president’s brother. He was convicted in October of operating as a major cocaine trafficker. Authorities said he controlled drug labs in Honduras and Colombia.

According to a criminal complaint against Fuentes Ramírez, Juan Orlando Hernández told ­Fuentes Ramírez that his brother Tony was in charge of trafficking operations in Honduras and that he should serve as the point of contact.

At Tony Hernández’s trial last year, prosecutors said he accepted $1 million in bribes from the notorious Mexican drug lord Joaquín “El Chapo” Guzmán — payoffs that were meant for the sitting Honduran president, they said.

“The defendant was protected by and had access to his brother, the current sitting president of Honduras, a man who himself has received millions of dollars in drug money bribes — bribes he received from some of the largest cocaine traffickers in the world, bribes he received from men like ‘El Chapo’ and the Sinaloa cartel who personally delivered $1 million to the defendant for his brother,” prosecutor Jason Richman argued in court, according to an Associated Press account of the proceedings.

Hernández took office in 2014 and has met with senior U.S. officials multiple times, including with Vice President Pence in 2017 and 2018, and with then-Vice President Joe Biden in 2015, according to White House announcements.

Hernández has used such interactions to discuss corruption and the deadly Central American drug trade that has long plagued the region, through which South American drugs travel.

Devlin Barrett in Washington and Mary Beth Sheridan in Mexico City contributed to this report.