The captives, who had been held for about two years, met their families soon after they landed and were to be flown to Bogota.
The military had pledged to stop operations in the area of the handover and told the guerrillas that they would be given time to leave the site before helicopters arrived to take the captives to freedom.
But Jorge Enrique Botero, a reporter accompanying the mission, told local television networks that the operation was hounded by Colombian military overflights that resulted in a delay of about two hours.
The military overflights almost caused the operation to be aborted as they "caused a lot stress not only to us but to the Farc rebels in charge of the handover", he said.
Colombia's peace commissioner, Luis Carlos Restrepo, called the allegations baseless.
Al Jazeera's Mariana Sanchez, reporting from Villavicencio, said family members of other hostages had also gone to Villavicencio in the hope that their loved ones would be freed as well and there was a sense of anticipation that others would be freed.
Alan Jara, a former governor, and Sigifredo Lopez, a former legislator, are set to be released by Wednesday.
Farc, which has been fighting the Colombian government for 45 years, was keen to release the hostages to restore some of its lost credibility, our correspondent said.
"There is a lot of rejection among the Colombian people and among the international community for using hostages as bargaining tools with the Colombian government," she said.
"They need to find a way to reposition themselves so they can continue this war."
A number of Farc fighters were captured in July when Colombian forces posing as humanitarian workers rescued 15 hostages, including Ingrid Betancourt, a French-Colombian politician, and three US military contractors.
The guerrillas are believed to have been weakened by a sustained Colombian military effort supported by $4bn from the US for sophisticated surveillance, communications intercepts and other tools.
Carlos Lozano, the editor of the communist weekly Voz, said the group was releasing the hostages because "they are heeding a call by society by showing flexibility and making a political gesture".
But Andres Pinate, a former Colombian defence vice-minister, told Al Jazeera that "we should not believe this is a great gesture of Farc".
"If they really were genuine they would come out and condemn the practice of kidnapping but they continue to keep dozens of people for economic gain, and many of them have been held for many, many years.
"It is inhumane, and there is nothing politically motivated by their actions, it's merely for monetary reasons."