Colombians have rejected a peace accord that would have ended a 52-year war with Marxist rebels, with a majority voting against the deal in a referendum.

Key points: Vote turnout is only 37 per cent, perhaps owing to torrential rain

Vote turnout is only 37 per cent, perhaps owing to torrential rain President Juan Manuel Santos accepts result, says ceasefire will continue

President Juan Manuel Santos accepts result, says ceasefire will continue Rebel leader says insurgent group maintains desire for peace

Opinion polls had shown the "yes" vote would comfortably win, allowing leaders to implement the deal painstakingly negotiated over the past four years to end the longest-running conflict in the Americas.

But Colombian voters confounded that forecast, with the deal being rejected by a tiny margin of 50.23 percent to 49.76 as votes were counted from 99.59 percent of voting stations.

Voter turnout was only 37 per cent, perhaps partly owing to torrential rain through the country.

President Juan Manuel Santos accepted the result, but said a ceasefire would continue — he had previously said his government would go back to war if the deal was rejected.

Mr 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.

"I will not give up, I will keep seeking peace until the last day of my term because that is the way to leave a better nation for our children," Mr Santos said.

Rebel leader Rodrigo Londono, who uses the nom de guerre Timochenko, said on Sunday the insurgent group maintained its desire for peace despite the failure of the plebiscite.

"The FARC reiterates its disposition to use only words as a weapon to build toward the future," Mr Londono said.

"To the Colombian people who dream of peace, count on us, peace will triumph."

Opponents of the pact believed it was too soft on the FARC rebels by allowing them to re-enter society, form a political party and escape traditional jail sentences.

President calls for end to 52-year war

The vote asked for a simple "yes" or "no" on whether Colombians support the accord signed last Monday by Mr Santos, who has staked his legacy on peace, and the rebel commander known as Timochenko.

"We must end a 52-year war and open the way to peace, a peace that will take us to a better future ... peace is the way to ensure our children and grandchildren have a better country," Mr Santos said after voting.

The Revolutionary Armed Forces of Colombia, known as FARC, whose numbers were halved to about 7,000 in recent years because of a US-backed military offensive, has agreed to turn in weapons and fight for power at the ballot box instead of with bullets.

After four years of negotiations in Havana, the final agreement was applauded around the world.

Influential former President Alvaro Uribe led the "no" camp, arguing that rebels should pay for crimes in jail and never be given congressional seats.

Under the accord, the FARC, which began as a peasant revolt in 1964, would have been able to compete in the 2018 presidential and legislative elections, with 10 unelected congressional seats guaranteed through 2026.

It would have given up its role in the lucrative illegal drug trade, and participated in reforming rural Colombia, most of which is poor and undeveloped.

Reuters