Five drivers working for a firm contracted to the agency have been killed this year and four aid workers have been kidnapped.
"WFP does not believe his death to be related to the recent spate of targeted attacks on aid workers in Somalia," WFP said in a statement.
Marcus Prior, a WFP spokesman, told The Associated Press news agency that Mohamed was off duty and was not in a marked agency vehicle when he was abducted.
Kidnappings and killings are common in the Horn of Africa nation, some attacks are political but others are the result of lawlessness in a desperately poor country awash with weapons.
The fighting between the Ethiopian-backed government and anti-government fighters in Somalia has forced many aid groups to scale back their operations despite a humanitarian crisis that aid workers say may be the worst in Africa.
More than 8,000 civilians have been killed and at least one million uprooted by the violence since early last year, and their plight has been compounded by record high food prices, hyper-inflation and drought.
WFP said experts fear that the number of Somalis needing food aid could reach 3.5 million people later this year, nearly half of the country's population.