Hundreds of people have been arrested after the tally from last Sunday's presidential race stalled without a clear victor and opposition leaders accused the Government of trying to steal the election.
Hernandez held a lead of more than 46 000 votes over Nasralla before the last-stage count.
Disputed votes could swing the outcome.
Venezuelan President Nicolas Maduro accused the United States of backing vote fraud in Honduras, while the top official at the USA embassy praised the peaceful protests and the "orderly" final count then under way.
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David Matamoros, who heads the electoral tribunal and is a member of Hernandez's party, did not declare a victor, saying parties could still file legal challenges and a wider recount is possible.
As the ballot count entered its sixth day on Saturday, the national police force said a 19-year-old woman was shot dead at a protest supporting opposition candidate Salvador Nasralla by gunmen who witnesses say were police. The report was not immediately confirmed by police.
The government has suspended "constitutional guarantees", given the army powers to patrol the streets and imposed a 6pm-6am curfew.
But mistrust mounted amid odd delays in the vote count and the sudden reversal of Nasralla's early lead.
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The tribunal began the partial recount on Sunday. Alliance officials have "slammed the decision as inadequate and said it would not attend the recount or accept the results", The Guardian says.
"So, the whole world will not recognise these elections."
Mr Hernandez, 49, implemented a military-led crackdown on gang violence that was backed by the United States and is credited with curbing the country's murder rate.
Nasralla, 64, is one of Honduras' best-known faces and is backed by former President Manuel Zelaya, a leftist ousted in a coup in 2009.
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