The United Nations children's agency warned that 275,000 of those children were expected to be so severely malnourished that they could easily die.
Severe acute malnutrition is the most extreme and visible form of undernutrition, with victims often appearing skeletal and frail, and in urgent need of treatment to survive.
Such children "are nine times more likely to die of cholera, or diarrhoea or measles," UNICEF spokeswoman Marixie Mercado told reporters in Geneva.
The World Health Organization warned last month that the drought was fuelling an outbreak of cholera and acute diarrhoea in Somalia that has already killed hundreds of people.
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The warning comes as Somalia faces the threat of its third famine in 25 years of civil war and anarchy.
At least 260,000 people died in the 2011 famine in Somalia - half of them children under the age of five, according to the UN World Food Programme.
The dire drought and food situation has forced more than 615,000 people to flee their homes since last November, in a country where 1.1 million people are already internally displaced.
Unicef's representative in Somalia, Steven Lauwerier, cautioned in a statement that women and children on the move especially "are extremely vulnerable".
Women and children who move about in search of assistance "are often robbed or worse, both on the way to and in camps," the statement said.
The UN has appealed for USD 720 million to provide aid to Somalia this year, of which it so far has received USD 415 million, or about 58 per cent, UN humanitarian agency spokesman Jens Laerke told reporters.