The top commander of Colombia's largest rebel movement was hospitalised on Sunday following a stroke and remains in intensive care, just days after his group handed over the last of its individual weapons as part of a historic peace deal.

Rodrigo Londono, better known by his nom de guerre Timochenko, checked himself into a hospital emergency room in the city of Villavicencio shortly after 8am (13:00 GMT) with slurred speech and numbness in his arm, doctors said in a news conference.

They said he remains in intensive care as a precautionary measure but his speech and mobility have already recovered 90 percent from what they described as a temporary blockage of blood flow to his brain.

Doctors said if there are no complications the leader of the Revolutionary Armed Forces of Colombia (FARC) could be released in the next 24 to 48 hours.

"Of course he's conscious and making jokes," another rebel leader known by his alias Pastor Alape said at the press conference.

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Londono, who is in his 50s, has suffered a number of health scares of late, the result partly of a lifetime in jungle trenches. Recently the FARC confirmed that in 2015 Londono suffered a heart attack during peace negotiations in Cuba, and earlier this year after the deal was inked had another unspecified medical setback for which he received treatment on the island.

Alape said Londono initially brushed off the symptoms and had to be convinced by his comrades to undergo medical evaluation.

"Thank you to everyone who is concerned about my health," Londono said on Twitter. "Everything is going well. I also thank the medical team for their care."

Londono's hospitalisation comes less than a week after Colombia reached a major milestone on its road to peace with the FARC rebels relinquishing some of their last weapons and declaring an end to their half-century rebellion.

The historic step was taken by Londono along with President Juan Manuel Santos at a demobilisation camp in Colombia's eastern jungles near Villavicencio.

Though hundreds of FARC caches filled with larger weapons and explosives are still being cleared out, the United Nations has certified that all individual firearms and weapons, except for a small number needed to safeguard the soon-to-disband camps, have been collected.

The step put Colombia closer to turning a page on Latin America's longest-running conflict, which caused at least 250,000 deaths, left 60,000 people missing and displaced more than seven million.

On Friday, the UN special representative in Colombia said the most urgent challenge in the country following the handover of the last weapons by rebels is to reintegrate the 10,000 former combatants into society.

Jean Arnault told the UN Security Council that members of FARC have "a deep sense of uncertainty" about their physical security following their disarmament and their economic future.