The Somali staff travelling along with the two foreigners were later released.
Michel Peremans, a spokesman for the aid agency, confirmed that two workers were missing, but would not say if they had been kidnapped.
"When we lose contact with teams we can't give much information because it can give problems afterwards," he said.
"I hope you can understand that this is too delicate, too problematic at this stage."
A total of 35 aid workers were killed in Somalia in 2008 and 26 abducted, the United Nations says.
The attacks have limited the ability of relief agencies to respond to one of Africa's longest humanitarian crisis.
More than three million Somalis - nearly half the population - depend on emergency food aid in a country that has been without an effective central government since 1991.
The Bakol region, near the Ethiopian border, is under the control of an armed opposition group that is fighting Somalia's weak UN-backed government.