The three employees of the French aid group Action Against Hunger (ACF) were released on Saturday after being held in Somalia since July.
The three, an American, a Zimbabwean and a Pakistani, boarded a plane in the southern town of Luq and were expected to head to Nairobi.
About 10 armed men were reported to have taken them from their office in Mandera, a remote area on the Kenyan border, on July 17.
Sheikh Ali Hussein from rebel group Hizb ul-Islam in Gedo province told the AFP news agency "a small plane flew the hostages out of the airport at Luq after they were freed by their kidnappers."
He said Hizb ul-Islam, which controls the region, had authorised their departure but had nothing to do with their kidnapping.
Al-Shabab, the main armed anti-government group, which controls much of Somalia's south, has also said it had nothing to do with the abduction of the three.
Hussein said he had reports that a ransom had been paid for the release of the hostages, which a local elder who declined to be identified estimated at $2.5 million.
Source: Al Jazeera (English)