Four Indigenous children who were missing for more than five weeks in a jungle in Colombia's south following a deadly plane crash arrived in the capital Bogota early on Saturday for medical treatment.

The siblings were found on Friday in Colombia's Caqueta province according to the country's armed forces and were initially treated by military medics who had been among the search teams searching for them.

The mission to find the four siblings, called Operation Hope, captured the imagination of Colombians as reports of clues to their whereabouts fueled longing they would be found safely despite spending more than a month in the inhospitable jungle.

"We did everything necessary to make the impossible possible, using satellites, using aircraft that launched messages, that launched food, that launched flyers, that launched hope," General Pedro Sanchez, commander of the military's joint command for special operations said at an air base in Bogota.

In photos shared by Colombia's military, the four children - three girls and a boy - appeared gaunt as they were being cared for by rescuers.

After the plane carrying the children landed in Bogota, four ambulances were waiting at to collect them and take them to a military hospital for specialist medical care.

They had been missing in the jungle since a Cessna 206 carrying seven people on a route between Araracuara, in Caqueta, and San Jose del Guaviare, a city in Guaviare province, issued a mayday alert due to engine failure in the early hours of May 1.

Three adults, including the pilot and the children's mother, died in the crash and their bodies were found inside the plane. The siblings, aged 13, 9, 4, as well as a now 12-month-old baby, survived the impact.