The world body said that the threats, coupled with insecurity after the murder of an elderly Italian nun in the capital and an attempt to assassinate the president of the weak government last month, prompted the move.
"Given the insecure environment and subsequent direct written threats against UN staff, a decision was taken to temporarily relocate all UN international staff members from southern and central Somalia," it said.
In addition, the UN said that it had suspended "until further notice" all of its missions to the capital of Mogadishu.
It did not say how many staff or missions to Mogadishu were affected.
No group has claimed responsibility for either the murder of the nun at a Mogadishu hospital September 17 or the car bomb bid the next day to kill interim Somali President Abdullahi Yusuf Ahmed in the government's temporary seat of Baidoa.
However, there are widespread suspicions of Islamist involvement in the two attacks and the United Nations said that it was concerned for the safety of their staff, given threats made by elements associated with the movement.
"Shortly after, the UN received direct written threats against its staff in Somalia," it said in its monthly report on activities in Somalia released by its office in Nairobi. "Security assessments are presently underway to determine when international staff can return to Somalia," it said.
The Islamists seized Mogadishu from warlords in June after months of fierce fighting and have rapidly expanded their territory to include much of southern and central Somalia, posing a growing threat to the transitional government.
"The rapid expansion of the influence of the Islamic courts ... has posed a serious challenge to the status quo, the consequences of which could have serious access and security implications if responded to militarily," the UN report said.
It added that it was making contingency plans with other relief agencies to carry on humanitarian work in Somalia "given the possibility of wider conflict, which could pull in neighboring countries."
The Islamists have declared holy war against Ethiopia, which supports the internationally backed Baidoa government but has denied repeated eyewitness and Islamist claims of sending troops to protect the administration.
As tensions build, UN agencies are reporting a huge surge in the number of Somalis fleeing to neighboring Kenya in fear of large-scale war.
More than 30,000 Somalis have arrived in Kenya since the beginning of the year and the flow of refugees has jumped from between 300 to 400 per day last month to close to 1,000 per day in the past week.
Somalia has been without a functioning central authority since the ouster of strongman Mohamed Siad Barre in 1991 and the current administration, formed in Kenya in 2004, has been wracked with infighting and unable to assert control.
© 2006 Agence France-Presse