Honduran President Juan Orlando Hernandez was set to be sworn in on Saturday for an historic second term after prevailing last year in a bitterly disputed election that sparked deadly protests and international condemnation over alleged fraud.

Hernandez appeared set to lose the 26 November election until an abrupt halt in the vote count and a shift in the results, taking victory away from his centre-left rival, Salvador Nasralla.

The opposition cried foul and more than 30 people were killed in protests that persisted through January in the impoverished Central American country. Nasralla has called for continued demonstrations.

International observers said the election was marred by irregularities and the Organization of American States called for a new presidential vote.

However, Hernandez held firm and the result was eventually ratified by the country's electoral tribunal, which is led by an ally of the president. Soon after, Mexico and the United States backed the incumbent.

Following a contentious decision by the Supreme Court in 2015, Hernandez is the first president to be re-elected since the end of military rule nearly four decades ago.

Hernandez has pledged to maintain his hard-line strategy in the fight against the country's gangs despite human rights groups' allegations of abuses.

During his first term, the homicide rate fell by almost 50 per cent, but Honduras is still one of the world's most violent countries.