No shortage of weapons for sale on Mogadishu markets
The Somali man, who had been working for the UN Childrens' Fund (Unicef), has not been named.
However, one of his colleagues said he was seized by six men in a vehicle.
The identity of the kidnappers is still unclear.
The incident comes a day after UN Secretary General Kofi Annan said it was too dangerous for the UN to open an office in Somalia at the moment.
Aid workers targeted
It is thought to be the first time a UN staff member has been kidnapped in Somalia for about a year.
One report suggested the motive for the kidnapping was a car rental contract that had been cancelled by Unicef.
But there has been no official word from Unicef.
Since Somalia descended into clan warfare following the overthrow of Mohamed Siad Barre in 1991, aid workers have been the targets of gunmen in Somalia who kidnap, rob or kill them.
No end to fighting
Last week, a 70 year old Swiss woman, Verena Karer, who worked for a humanitarian agency, was killed at her home in the southern town of Merca.
In a report published on Wednesday, Kofi Annan said Somalia remained one of the most dangerous environments in which the UN operates, and that the security situation did not allow for a long-term presence.
The report was based on the findings of a security mission which went to Somalia in January, about 18 months after the fledgling interim government was set up.
More than a dozen people were killed in Mogadishu in fighting between rival factions in the Medina area on Monday and Tuesday.