Officials of the World Vision center in Baidabo said that their offices in the Wajid, Tiyaglo, and Baidabo districts were attacked on Tuesday.
The fighters seem to have taken some important documents from the offices and have also taken some vehicles belonging to World Vision, but it is not known where they have taken the vehicles, they added.
The leaders of al-Shabab have neither confirmed nor denied involvement in the attacks.
It is not the first time al-Shabab fighters have attacked the offices of international organizations conducting humanitarian assistance programs in southern Somalia.
The incident occurred shortly before World Vision officials were due to meet al-Shabab members in Baidoa to discuss the future of their operations.