President Juan Manuel Santos fails to win approval as voters balk at an agreement that included amnesty for war crimes

Colombians have rejected a peace deal to end 52 years of war with Farc guerrillas, throwing the country into confusion about its future.

With counting completed from 98.98% of polling stations, the no vote led by 50.2% to 49.8%, a difference of fewer than 54,000 votes out of almost 13 million cast. Turnout was low, with less than 38% of the electorate casting a vote.

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The verdict on the deal between the government of Juan Manuel Santos and the Farc, reached after four years of intense negotiations, means it cannot now be implemented.

Polls before the vote predicted that the yes camp would win with a comfortable 66% share. Santos had been confident of a yes result and said during the campaign that he did not have a plan B and that Colombia would return to war if the no vote won. His opponents, led by former president Álvaro Uribe, said a win for their side would be a mandate for the government and rebels to negotiate a “better agreement”.

Both government and rebels have repeatedly said that the deal was the best they could achieve and a renegotiation would not be possible.

Santos, who watched the results come in at the presidential palace in Bogotá, said he would send his negotiators back to Havana to meet with Farc leaders on Monday. “I will not give up,” he said in a televised address. “I will continue seeking peace until the last day of my presidency.”

He added that the bilateral ceasefire that has been in place since 29 August would continue.

Santos, who has staked his legacy on achieving peace, said he would meet with all political parties on Monday to find a way forward for the peace process. The vote would not affect Colombia’s stability, he said.

The Farc leader, Rodrigo Londoño, said the insurgent group maintained its desire for peace despite the failure of the plebiscite to approve its recently signed deal with the government.

“The Farc reiterates its disposition to use only words as a weapon to build toward the future,” said Londoño, who is known by his nom de guerre, Timochenko. “To the Colombian people who dream of peace, count on us, peace will triumph.”

Fernando Giraldo, a political analyst, said the fact that both the government and guerrillas reiterated their commitment to peace was a good sign but the future was unclear. “The plebiscite laid everything out in black and white and now we’re stuck in a grey area,” he said.

Under the agreement rejected by voters, the Farc’s 5,800 fighters and a similar number of urban militia members would have disarmed and become a legal political party. Whether or when that will happen now is unknown.

The deal would have allowed rebel leaders to avoid jail if they confessed to their crimes such as killings, kidnappings, indiscriminate attacks and child recruitment, something that many Colombians found hard to swallow.

By promoting a no vote, Uribe argued that he did not support continued war but wanted to fix the agreement. “Colombians, let’s correct the path,” he said after the final results of the vote were announced. “We insist on correctives so that the constitution is respected, not substitutes, [that there be] justice, and not the derogation of institutions, political pluralism without it appearing to be a prize for criminals,” he said.

Both the Farc and the government had believed that the deal that had been reached, which had overwhelming international support, had struck a balance between all those factors.

Facebook Twitter Pinterest Supporters of the peace deal watch the results of the referendum in Cali on Sunday. Photograph: Guillermo Legaria/AFP/Getty Images

“Although imperfect, the agreement represented a concrete way forward for peace and justice,” said Erika Guevara-Rosas, Americas Director at Amnesty International. “It’s imperative that Colombia does not walk away from this project and that the country continues to move towards the long-awaited peace millions are longing for.”

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In a ceremony on 26 September, with the UN secretary general, Ban Ki-moon, US secretary of state, John Kerry, and a dozen Latin American leaders on hand as witnesses, Santos and Timochenko signed the deal their negotiators had reached after four years of talks in Havana.

In the days before the vote, the Farc commanders rushed to make public apologies to their victims in an attempt to boost support for the yes vote. On Thursday, chief rebel negotiator Iván Márquez presented the community of Bojayá, Chocó, where the 2002 bombing of a church killed 119 people, with a new crucifix. At a similar event on Friday in Apartadó, Antioquia, the site of a 1994 Farc massacre of 35 people, Márquez said it “never should have happened”.

On Saturday UN monitors oversaw the Farc’s destruction of more than 620kg of explosives in a remote corner of the country. The group also promised to give an account of their assets, to be used to compensate victims of the war, despite having previously said they had no money.

But the apologies and promises appear to have come too late to sway voters. “The day they are behind bars I will go and give them my hand and forgive them,” said Nohora Tovar, a senator with Uribe’s Centro Democratico, who was kidnapped by the Farc in 2000.