Right-wing parties opposed to a peace deal with the FARC won historic elections in Colombia.

Right-wing parties opposed to a peace deal with the FARC won historic elections in Colombia Sunday but fell short of a majority in polls that saw the former rebels enter the Congress.

The hardliners' victory raises questions about the future of the peace agreement signed with President Juan Manuel Santos in November 2016.

Santos said the polls were "the safest, most transparent elections" in the country's recent history, with the FARC spurning jungle warfare for politics, and the ELN — the country's last active rebel group — observing a ceasefire.

"This is the first time in more than half a century that the FARC, instead of sabotaging the election, are taking part in it," he said, adding that the ELN had "respected" their ceasefire.

The Centro Democratico party of ex-president and senator Alvaro Uribe, a fierce opponent of the peace agreement, polled the most votes, winning 19 seats in the Senate and 33 in the lower house.

But centrist and leftist parties also polled strongly to deprive the right of a majority.

The peace accord with the now-renamed Revolutionary Armed Forces of Colombia (FARC) guarantees their new political party 10 of the 280 seats in the new Congress, five in the Senate and five in the Chamber of Deputies.

More than 260,000 people were killed in more than five decades of armed conflict between the Farc and other rebels, government forces and right-wing.