Action Against hunger have said that four of their staff were taken, without giving their nationalities.
The European Commission spokesman said: "It was a flight under contract to the EU Commission. It was an Action Contre la Faim operation."
The lawless east African nation has been the scene of a succession of kidnappings in 2008, with humanitarian workers increasingly targeted.
Clan militias and Islamic fighters fighting the government are typically alleged to be involved in the abductons.
However, the fighters regularly refute these claims, saying that the government of President Abdullahi Yosuf undertake the attacks and place the blame on them.
There has been no central government in the country since 1991, when Mohamed Siad barre was overthrown.
The country has since fallen into violent disorder, with drought and rising food prices contributing to what some are calling a humanitarian disaster. Few aid organisations are able to work in the country at present.
Abductions often occur to extract ransoms. Two Italians, one Kenyan and one Briton are currently being held by gunmen after being abducted in April and May.
Action Against Hunger has 14 foreign and 219 local employees in Somalia.