Local media on Wednesday quoted elders in the town of Baidoa as saying heavily armed Islamist fighters stormed the UNICEF office and detained Ali Moalin Black, the head of security at the office.
The fighters of the rebel group which controls much of south and central Somalia, where the Horn of Africa drought is the worst hit, also arrested Abdelrasak Mohamed, an officer with the International Committee for the Red Cross (ICRC) after raiding his home in the town of Baidao, a stronghold of the insurgent group.
Al Shabaab said last week lifted the ban it imposed in 2009 on the operation of humanitarian agencies working in areas under their control to deal with the worsening humanitarian situation.
The group barred aid agencies after they accused them of being involved in what they termed as anti-Islam activities, a claim then strongly rejected by relief agencies.
Severe drought has forced thousands of desperate and hungry Somalis into overcrowded refugee camps in neighboring Kenya and Ethiopia, as well as into the chaotic Somali capital of Mogadishu, where hundreds of families arrive every week seeking food and shelter.
It was not immediately clear why the Islamist rebels arrested the aid workers who were reportedly staying in the town since the ban on aid agencies was imposed two years ago.
The radical group has not officially commented on the arrests.
Somalia is the hardest hit by the drought which also affected the whole of Horn of Africa region. The UN describes the situation in the war-torn country as the world's worst humanitarian crisis as parched land and dried pasture due to three consecutive failed rains ruined livestock and crops, the mainstay of family economy in Somalia.