One of them was the country’s electoral commission, which reported on election night that the main opposition candidate, Salvador Nasralla, was ahead before the electronic count stopped for a day and a half. When it resumed, the trend reversed direction to favor Mr. Hernández, and he was eventually declared the winner by about 50,000 votes.
“When you have an election that is very close, you have to trust the judge,” said Miguel Calix, the Honduras representative for the Netherlands Institute for Multiparty Democracy, a pro-democracy organization backed by Dutch political parties. “And the problem is that nobody trusts the judge.”
But with Mr. Hernández winning only a plurality in the multiparty election, the result has prompted widespread street protests that have turned deadly.
“The people are indignant and they are rising up,” said Edmundo Orellana, a former justice minister and constitutional law professor at the National Autonomous University of Honduras. “The intensity of the protests will not fall.”
An election observer mission from the Organization of American States concluded on Sunday that there were so many irregularities and deficiencies that it was impossible to be sure of the winner. Luis Almagro, the organization’s secretary general, called on the Honduran government to schedule a new election.
Both the alliance backing Mr. Nasralla and the opposition Liberal Party have asked for the results to be annulled.
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Mr. Nasralla traveled to Washington this week to seek support, but he appeared to acknowledge that his fight was over on Friday, admitting that he had “no confidence” in the effort to have the result voided.
Although large demonstrations have been peaceful, in some areas people have blockaded roads, burning tires and tree branches in protest. Security forces have used tear gas and live ammunition in response.
Late this week, police officers and soldiers were deployed in large numbers to clear blockades set up by protesters in the capital and the north of the country.
A statement on Wednesday from human rights experts at the United Nations and the Inter-American Commission on Human Rights said that at least 12 people had been killed. Hundreds more have been detained at military installations, where they have been “brutally beaten,” the statement said.
Representative Jim McGovern, Democrat of Massachusetts, said in a statement on Friday that he was “angry and deeply disturbed” by the State Department’s recognition.
“Very few Hondurans have confidence in the results, and the country remains deeply polarized,” said Mr. McGovern, who was among nearly 50 lawmakers who signed letters urging the United States to back the O.A.S.’s position. “For the U.S. government to pretend otherwise is the height of blind folly and it will surely harm our influence and undermine our priorities throughout the region.”
The State Department acknowledged that the close result and the flaws identified by the O.A.S. and another observer mission from the European Union “underscore the need for a robust national dialogue.”