The Office for the Coordination of Humanitarian Affairs (OCHA) attributed the exodus from the Somali capital in September to insecurity stemming from fighting - resulting in many civilian casualties - between various anti-government groups and forces with the Transitional Federal Government (TFG), Ethiopia and the UN-backed African Union Mission to Somalia (AMISOM).
Over 1,000 cases of diarrhoea have also claimed dozens of lives, and the UN World Health Organization (WHO) and its partners have stepped up their deliveries of medicines and other supplies.
IDPs have limited access to sanitation facilities, and many regions of Somalia face water shortages. Water is being trucked in for drought-stricken areas in the country's central region and there has only been sporadic rainfall, OCHA said.
Fighting continues to impede humanitarian operations, with UN flights into Mogadishu having been suspended following a ban by an Islamist insurgency group last month. In spite of this, the WFP and other aid agencies have been able to feed almost 2 million people.
Earlier this week, Secretary-General Ban Ki-moon deplored the recent killing of aid workers in Somalia, where two local staff members of UN agencies have been killed since Friday.