Honduran centrist candidate Salvador Nasralla alleged fraud in the country's highly contested presidential vote after his Trump-backed rival Nasry Asfura pulled narrowly past him overnight.

Nasralla, in a post on X on Thursday, said the screen displaying the vote data went blank at 3.24am and alleged "an algorithm changed the data", giving the higher tally to Asfura after Nasralla had been leading the vote count since Tuesday.

The results are being updated on the electoral body's website.

The run-up to the vote in the small Central American country had been rocked for months by allegations of fraud.

The election was catapulted to the international stage as US President Donald Trump threw his support behind Asfura and alleged, without evidence, that there had been possible fraud in the initial vote tally.

The CNE national electoral council defended the process and said voting records considered inconsistent were not part of the formal count and would be reviewed.

"There are cases where the records of the polling stations have presented insurmountable inconsistencies," said CNE head Ana Paola Hall, adding the recount would require time but be delivered within the legal deadline – December 30.

"The results delivered by the CNE will be final," she added, calling for patience.

"Haste is sometimes the enemy of legitimacy."

Late on Thursday, CNE official Marlon Ochoa gave a press conference in which he criticised the electoral process for problems with the vote publication system, alleged vote-buying and intimidation, as well as the "vulgar foreign intervention."

"I believe there is unanimity among the Honduran people that we are perhaps in the least transparent election in our democratic history," Ochoa said, decrying an electoral "coup".

On Thursday, the National Party's Asfura held 40.25 percent, nearly 23,900 votes ahead of the Liberal Party's Nasralla, who had 39.39 percent.

Rixi Moncada of the ruling leftist Libre Party remained well behind in third place in the election, which was held on Sunday.

With around 87 percent of the tally sheets counted, each representing votes from a single polling station, Asfura held a slim lead which narrowed slightly through the day.

Around 17 percent of the tally sheets have inconsistencies and will be reviewed, according to the country's electoral authority.

Nasralla's post did not provide evidence of vote tampering.

"They must investigate the Colombian company involved in these changes, ASD," he said.

Fraud allegations have haunted Honduras since the fiercely contested 2013 presidential election, when opposition leaders accused the ruling party of manipulating vote tallies and violating campaign finance rules in a race marred by irregularities. (Reuters)