A final vote tally by Bolivia's electoral board gave President Evo Morales an outright win in the first-round election on Thursday, with 47.07 per cent of ballots compared to 36.51 per cent for runner-up Carlos Mesa, data on the board's website showed.

Morales's 10.56 point lead with 99.99 per cent of votes counted means he does not have to face Mesa, a former president, in a riskier second round run-off, after a disputed race in which the opposition alleged fraud and Morales has accused rivals of staging a "coup."

A spokesperson for Bolivia's electoral board said 0.01 per cent of votes have been voided in the region of Beni with new voting there scheduled for November. She added they are not enough to change the outcome. The president of the electoral office in Beni said a little over 500 people will vote again due to the annulments.

With the official result, Morales, already Latin America's longest-serving president, wins a fourth term in a row, allowing him to govern the landlocked South American country through 2025 for a total of 19 years.

The Andean nation has been on a knife edge since the close and bitterly disputed vote, while international vote monitors expressed concern about an earlier unexplained daylong gap in reporting results before a sudden spurt in Morales's vote percentage. Opposition backers continued to stage rowdy protests since the vote, while Morales's backers staged a march in the capital to show their support for the president.

Opposition presidential candidate Carlos Mesa has said 'it's clear that there's a gigantic fraud going on.' (Jorge Bernal/AFP/Getty Images)

Morales has repeatedly said he won outright and his opponents are conspiring to oust him. He earlier said that a quick count of the vote also gave him a first round win.

"I want to denounce to the people and the world that a coup d'etat is underway," Morales said at a news conference Wednesday. "The right wing has prepared it with international support."

Morales did not specify where the alleged international support for the coup was coming from, but he regularly rails against U.S. imperialism in Latin America.

Protesters stand amid tear gas fired by police during a protest against the re-election of Morales on Wednesday night in La Paz. (Juan Karita/The Associated Press)

He cited the burning by protesters of electoral offices in two cities where votes are being tallied as proof of the coup. Protesters also burned ballots in a third city.

Suspicions of electoral fraud rose when officials abruptly stopped releasing results from the quick count of votes hours after the polls closed Sunday with Morales topping the eight other candidates, but also falling several percentage points short of the percentage needed to avoid the first runoff in his nearly 14 years in power.

Twenty-four hours later, the body suddenly released an updated figure, with 95 per cent of votes counted, showing Morales just 0.7 percentage point short of the 10-percentage point advantage needed to avoid a run-off.

Venezuela supports Morales

That set off an uproar among the opposition and expressions of concern by international monitors.

The observer mission of the Organization of American States asked for explanations and the European Union and the UN expressed concern about the electoral process and called for calm. The United States and Brazil, among others, also expressed concerns.

Michael G. Kozak, acting U.S. assistant secretary of state for the Western Hemisphere, warned Wednesday that Bolivian authorities will be held accountable if the process isn't fair.

"I think you will see pretty strong response from the whole hemisphere, not just the U.S.," Kozak said during a House hearing.

A Morales supporter shows her support during a march in La Paz on Wednesday. (Juan Karita/The Associated Press)

In Caracas, Venezuela's socialist president, Nicolas Maduro, voiced support for his ally Morales.

"It is a coup d'etat foretold, sung and, one can say, defeated," he said.

The crisis was aggravated by the resignation of the vice president electoral council, Antonio Costas, who said he disagreed with the decision to interrupt transmission of the vote count.

On Tuesday, the Andean nation saw a second night of violent protests in several cities. Then on Wednesday, a strike that mostly affected transportation erupted in Santa Cruz, the most populous eastern region and an opposition stronghold, while Morales supporters clashed with his foes in one of the city's slums.

Protesters in other regions announced that they would join to demand respect for the vote.