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The Somali army has warned people not to return home in the parts of the capital, Mogadishu, which was recently abandoned by Islamist militants.
Gen Abdikarim Yusuf Dhagabadan, the deputy army chief, said the areas were mined and not fully secure.
Al-Shabab, which controls much of central and southern Somalia, announced over the weekend it was withdrawing from Mogadishu for tactical reasons.
Thousands of famine victims have been fleeing its territory since June.
Many of them have been arriving in search of food in Mogadishu, which is now controlled by the weak interim government and by a 9,000-strong African Union force (Amisom).
Al-Shabab banned many aid agencies from areas it rules two years ago.
An estimated 12 million people in the Horn of Africa have been affected by the region's worst drought in 60 years.
Rubble and trees
The BBC's Mohamed Mwalimu in Mogadishu says some al-Shabab fighters remain in some parts of the city and sporadic shooting continues.
But civilians are returning to the four northern districts previously occupied by them, despite the army's warning, he said.
Government troops and African peacekeepers are now in these areas trying to help repair roads and the trenches used as defensive positions by the militants.
Our reporter says it is a shock to see these old districts of the city reduced to rubble with trees growing everywhere.
However, those residents returning to the al-Shabab areas were happy to be returning home, he says.
Extended drought is causing a severe food crisis in the Horn of Africa, which includes Kenya, Ethiopia, Djibouti and Somalia. Weather conditions over the Pacific means the rains have failed for two seasons and are unlikely to return until September.
An estimated 12.5 million people in the region are affected by the drought. The UN has declared a famine in five areas of southern Somalia, where 50% of children are acutely malnourished and four children out of every 10,000 are dying daily.
The humanitarian problem is made worse by ongoing conflicts. Militants had lifted a ban on aid agencies operating in parts of southern Somalia, but now say reports of famine are exaggerated and have again limited access.
Since the beginning of 2011, around 15,000 Somalis each month have fled into refugee camps in Kenya and Ethiopia looking for food and water. The refugee camp at Dadaab, in Kenya, has been overwhelmed by an estimated 400,000 people.
Farmers unable to meet their basic food costs are abandoning their herds. High cereal and fuel prices had already forced them to sell many animals before the drought and their smaller herds are now unprofitable or dying.
The refugee problem may have been preventable. However, violent conflict in the region has deterred international investment in long-term development programmes, which may have reduced the effects of the drought.
Development aid would focus on reducing deforestation, topsoil erosion and overgrazing and improving water conservation. New roads and infrastructure for markets would help farmers increase their profits.
The result of climate conditions, conflict and lack of investment is that 6.7 million people in Kenya and Ethiopia are currently existing on food rations, and relief agencies estimate 2.6 million in Somalia will need assistance a new emergency operation.
"I'm a resident of Abdul Aziz district. I was forced out of my home for almost two years and today I'm overwhelmed with joy coming back," one man told the BBC.
Another woman also expressed her joy.
"I was living in a camp for displaced people in a former building of the American embassy. I am happy today and we hope the government will succeed," she said.
Our correspondent says it is first time he has seen Mogadishu residents so fully supportive of the government - and to his surprise some of them brought food and water to the soldiers patrolling the area.
Meanwhile, the UN World Health Organization has warned of a cholera epidemic in Somalia - where there are now a total of five famine zones.
"The concern here is the root causes of cholera, and that is related to water and sanitation," AFP news agency quotes WFP adviser Michel Yao telling reporters in Geneva.
"And with the IDPs and population movement, this increases the risk of further spread of the disease, and that is our fear," he said.
Some 100,000 people have arrived in Mogadishu in the last two months in search of food.
The UN says 3.2 million people - almost half the population - are in need of immediate life-saving assistance in Somalia, which has been wracked by civil war for two decades.
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