Colombia’s historic presidential election is heading into a runoff vote, with right-wing candidate Ivan Duque leading the race but failing to secure the majority needed to win outright.

With nearly all of the votes counted, Duque – who led opinion polls ahead of Sunday’s election – was first with 39.1 percent.

He will now face leftist candidate Gustavo Petro, who finished second with 25.1 percent, in the second round of voting on June 17.

Former Medellin Mayor Sergio Fajardo, a centre-left candidate, came third with 23.8 percent.

Al Jazeera’s Lucia Newman, reporting from the capital, Bogota, said the prospect of Duque finishing first in an election headed to a runoff vote was widely anticipated.

She added, however, that the centre and centre-left had done far better than opinion polls had suggested, pointing to Farjado’s better-than-expected showing in the election.

The winner of the second round will begin a four-year term in office from August onwards.

Around 36 million Colombians were eligible to vote. The final outcome of the elections is expected to shape the future of a controversial 2016 peace deal between the government and FARC rebels.

‘Extraordinary feat’

Incumbent President Juan Manuel Santos, who won the Nobel Peace Prize for ending a decades-long conflict with FARC, was ineligible to run for re-election having served the maximum two terms permitted by Colombia’s constitution.

He described the vote as the calmest and “most secure” in the country’s recent history.

“So far not a single voting station has had to be moved for security reasons … It’s been many decades since that has happened,” he said in a televised address after casting his ballot in Bogota.

As long lines of voters amassed in polling stations across Bogota on a cloudy day, Al Jazeera’s Newman said the election’s peaceful conditions marked “an extraordinary feat and something that Colombians have never seen” in recent times.

Casting his ballot in Bogota, Duque called Sunday “a very special day for our nation”.

“I want a country of legality, a full-on fight against corruption, a country where peace can breathe throughout the land,” he said.

Ivan Duque called Sunday’s vote marked a ‘very special day for’ Colombia [Nacho Doce/Reuters]

Irregularity accusations

In the run-up to the vote, Petro had accused officials of failing to address a voting software glitch that he said could lead to fraud.

Colombia: Can leftist Gustavo Petro become president?

He reiterated those concerns on Sunday after casting his vote, urging citizens to document any irregularities with their phones.

His campaign also issued a statement alleging voting irregularities, including votes pre-marked in favour of Duque.

“Petro is claiming there is an effort under way to deprive him of victory by an adjustment of the electoral software,” said Al Jazeera’s Newman.

“The outcome [of the vote] could be questioned, especially if it is very close.”

‘Colombians want peace’

The deal with FARC, pushed through by Santos in November 2016 after it was rejected in a referendum vote weeks earlier, brought to an end to the conflict which killed 220,000 people and displaced nearly seven million.

The deal allowed FARC to rebrand as a political party – the Common Alternative Revolutionary Force – and guaranteed it five seats in each of the country’s two chambers of parliament, regardless of vote share.

Many Colombians however felt the agreement was too lenient on FARC by allowing its members to enter politics and avoid imprisonment and face reduced sentences for crimes committed during the conflict.

Both Duque and Petro have criticised the peace deal, with the former pledging to pass reforms undoing key aspects of the agreement and the latter alleging it has done little to achieve lasting social reform.

FARC did not field a candidate in the presidential election after leader Rodrigo Londono – commonly known as Timochenko – pulled out of the ballot due to health problems.

After voting in elections for the first time, Londono told reporters in Bogota that the majority of Colombians “want peace”.

“The invitation is for everyone to exercise this right and to make today a day of reconciliation,” the leader of FARC also wrote on Facebook.