'Threats and harassment'
Peter Smerdon, a WFP spokesman, said the agency hopes to resume operations as soon as possible.
"We are the biggest humanitarian agency operating in Somalia and we've been doing so for many years, but finally the threats and attacks on our operations and harassment of our staff was getting too much," he told Al Jazeera.
"We are obviously deeply concerned about the welfare of the people of Somalia but the security of our staff is critical and thats why we've taken this step, which is very unfortunate."
Somalia has not had an effective government since 1991, when Mohamed Siad Barre was overthrown by armed groups who then turned on each other.
Members of Somalia's al-Shabab group and its allies, who are fighting to topple the UN-backed government, control much of southern and central Somalia.
Smerdon said al-Shabab fighters control 95 per cent of the territory where aid operations are now suspended.
"In November of last year, they set out 11 conditions for aid agencies to work in southern Somalia and these included such things as removing women from their jobs ... and demands for payment of $20,000 every six months for security.
"So there have been these unacceptable demands and at the same time we've had an escalating series of threats, which has forced us to pull out."