Challenger Salvador Nasralla has alleged fraud and said he won't respect the official results. He's watched an initial five-point lead diminish in recent days as official results have trickled out.
Last night, Hernandez was ahead by more than 45,000 votes with nearly 93 per cent of Sunday's votes processed. He had 42.9 per cent of the vote to Nasralla's 41.4 per cent.
Opposition supporters protested throughout the day and into the night outside the electoral court's facilities and on major boulevards, setting up roadblocks and lighting bonfires in the streets.
David Matamoros, president of the electoral court, said yesterday that officials had not finished counting in part because overnight they had to evacuate after tear gas drifted into the building.
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He said that about 2,000 electoral reports from polling sites contained "inconsistencies," including lacking signatures from members of the polling sites or not having seals. Those will most likely require a special count and it was unclear how many votes were at play in those cases, he said.
Honduras' influential Private Business Council urged the electoral court to wait until all the votes are counted before announcing the result.
Across the country, columns of smoke rose from tires set ablaze in the streets.
In Tegucigalpa, protesters and riot police faced off amid billowing clouds of gas. Officers with batons and tear gas closed two central boulevards, and water cannons were deployed for crowd control.
At least four people were admitted to the University School Hospital with injuries to the head and neck.
Red Cross workers also attended to people in the streets, including one young protester bleeding profusely from the head. In the northern municipality of Santa Rita, police reported that two officers and a member of the military were injured by opposition protesters.
The Public Safety Department warned that it would "peacefully clear out the protesters because they are blocking traffic." It reported more disturbances in at least eight cities besides the capital.
Many schools and universities in the capital announced they would be closed through the weekend to keep students out of harm's way.
The Association of Banking Institutions recommended branches close yesterday afternoon in anticipation of street clashes.
Nasralla via Twitter asked his supporters to continue to protest peacefully and not be provoked into violence. Luis Zelaya, candidate for the Liberal Party, who was running a distant third in the tally, called for his supporters to "defend democracy."
"That situation every day makes integration of society and the recovery of governability more distant," it said in a statement.
Former President Manuel Zelaya, whose Libre party was part of Nasralla's coalition, called for international observers to organise a public count of ballots to alleviate concerns of manipulation. He spoke on Honduras' Canal 5 television yesterday.
"That is a practical and definitive solution to exit the crisis Hernandez has gotten us into," said Zelaya, who was ousted from office in a coup orchestrated by Hernandez's National Party in 2009.