Early on Monday, electoral authorities said Hernandez had won 42.98 percent of the votes, compared with opposition candidate Salvador Nasralla’s 41.39 percent, based on 99.96 percent of the votes counted.
But the authorities stopped short of declaring a winner.
No reason was announced for why a winner was not declared, but the move may have been because of the widespread allegations of irregularities cited by Nasralla.
The small Central American nation of 10 million, which suffers from chronic violence and prolific gang activity, held the presidential vote last Sunday.
Tensions have been high since shortly afterwards. Nasralla was in the lead with a significant margin before a 24-hour hiatus in the official vote count reversed that trend last week. The opposition candidate soon alleged fraud and called on his supporters to take to the streets.
Tens of thousands took to the streets on Sunday in a show of support for Nasralla, a former TV star.
Authorities then restricted the freedom of movement in the country in an attempt to control widening unrest.
At least one person has been killed in clashes while hundreds more have been arrested by security forces.
On Monday, Hernandez, who would be starting his second term, called for peace and reconciliation.
“I make a call for peace, for brotherhood, for sanity, for national unity. My commitment to work for peace and tranquility of Honduras is more firm than ever,” he told reporters.
Nasralla, however, has demanded that one-third of the votes be recounted.
Meanwhile, the Organization of American States (OAS) cited irregularities and errors in the election process and called for a recount of as many votes.
“The tight margin, along with the irregularities, errors and systematic problems that have surrounded this election, does not allow the mission to be certain about the results,” said former Bolivian president Jorge Quiroga, heading the OAS election observation mission in Honduras.