In the trial, prosecutors and witnesses linked the president to the operation, although he was never charged and has denied wrongdoing. A separate federal indictment filed in Manhattan on April 30 accuses a former senior Honduran police commander, Juan Carlos Bonilla, of conspiring to import cocaine to the U.S. "on behalf of" President Hernandez, who allegedly benefited from the profits.
In the State Department's certification, the Tony Hernandez trial is mentioned only once and the Honduran president's connection is not mentioned at all.
A State Department official defended the findings while acknowledging high-level corruption remained a problem in Honduras.
"Extremely serious challenges remain, including credible information that the most senior levels of the government received money from narco-traffickers," said the official, from the Western Hemisphere affairs bureau, on condition of anonymity in keeping with administration protocol.
"Much work remains to be done in Honduras," the official said. "Without U.S. assistance, we would likely see backsliding on the progress that has been made."
Hernandez's government also drew international criticism for its decision to close down a highly regarded anticorruption agency sponsored by the Organization of American States. The agency had launched numerous investigations into powerful Hondurans and was successful in important prosecutions, including of a former first lady and former mayor of Tegucigalpa, the Honduran capital.
In January, Hernandez ignored pleas from international diplomats and civil rights organizations to not abolish the panel, known formally as the Mission to Support the Fight Against Corruption and Impunity in Honduras, or MACCIH.
At the time, State Department officials lobbied intensively for Hernandez to preserve the anticorruption group but ultimately were defeated.
MACCIH was modeled after a United Nations-created anti-corruption agency in Guatemala, which was similarly scoring investigative victories only to be closed down by then-President Jimmy Morales, who gave international investigators 24 hours to leave the country.
"What we see in Central America is a series of blows to the rule of law, as institution after institution intended to investigate corruption is shut down by the people being investigated," Rep. Norma Torres, D-Calif., the only Central America-born member of Congress, said when MACCIH was closed.