The clashes between government forces and the Al-Shabaab militia in Mogadishu also forced many more to flee from their homes.
The U.N. High Commissioner for Refugees says the developments emphasizes the need for governments "to assess asylum claims from people originating from central and southern Somalia in the broadest possible way."
"Where refugee status is not granted, UNHCR is advising governments to extend complementary forms of international protection, which would allow Somalis legal residence until conditions improve for safe return."
Many displaced Somalis endure "poor and degrading conditions" in the southern and central regions of the country. More than 300,000 out of Somalia's estimated 1.4 million internally displaced people are hunkered down in Mogadishu.
In its Friday briefing, the agency also addressed the deportations of Somali refugees and those seeking asylum from Saudi Arabia.
The refugee agency urged Saudi authorities to halt deportations on humanitarian groups because of the violence in Mogadishu.
About 1,000 Somalis were deported from Saudi Arabia in June and the tally for "reported forced returns" is close to 1,000, the refugee agency said.
Most of the deportees left Somalia because of "conflict, indiscriminate violence and human rights abuses," and most are women. Many have said they've worked in Saudi Arabia for some time.