A boy passes by electoral posters of an independent candidate in the presidential election in Bissau, Guinea-Bissau. File picture: Seyllou

Bissau - Former Finance Minister Jose Mario Vaz won a high-stakes presidential run-off election in Guinea-Bissau meant to draw a line under a 2012 coup, the elections commission said on Tuesday, but the losing candidate rejected the result.

The looming dispute over the outcome of Sunday's vote threatens to stir further uncertainty in the tiny, chronically unstable West African nation as it seeks to repair frayed relations with its regional and international partners.

Vaz, the candidate of the dominant African Party for the Independence of Guinea and Cape Verde (PAIGC), took 61.9 pct of votes, according to results announced by elections commission president Augusto Mendes.

He defeated Nuno Gomes Nabiam, an independent candidate who comes from the Balanta ethnic group - the country's largest - and is seen as close to the army. He garnered 38.1 percent of ballots, the commission said.

“I will not accept the result, because the figures collected by my campaign in four of eight regions are different from those announced by the National Electoral Commission,” Nabiam told journalists in the capital Bissau.

He was speaking after a meeting with Vaz, the country's current interim president, the incoming prime minister and Antonio Injai, the powerful head of the army.

Guinea-Bissau's last election in 2012 was abandoned after soldiers under Injai stormed the presidential palace just days before another PAIGC candidate, Carlos Gomes Junior, appeared poised for victory in a scheduled run-off.

Sunday's election was intended to end a transitional period that followed the military takeover.

An observer mission from the Economic Community of West African States (ECOWAS) said on Monday the voting itself was transparent and credible.

European Union elections observers had earlier said that voting on the day had taken place without major incident.

“The electoral process was long, but the first round was crowned a success as was the second round,” commission president Mendes said during the announcement of the results.

Turnout for the election was 78.1 percent, down from the nearly 90 percent recorded in last month's first round vote.

Guinea-Bissau's supreme court must now validate the election results before they become official. It is expected to do so in the coming days.

Weak state institutions, along with its maze of islands and unpoliced mangrove creeks, have made the former Portuguese colony a paradise for smugglers of Latin American cocaine destined for Europe.

Since Guinea-Bissau won independence in 1974, no elected leader has completed a five-year term and analysts say donors and regional powers who have been bankrolling the interim administration are frustrated with the recurrent crises.