NAIROBI, March 20 (Reuters) - Acute watery diarrhoea in Somalia has killed hundreds of people this year, the Minister of Health said on Tuesday as aid agencies warned the nation was in the midst of a cholera outbreak.

"The death toll is in the hundreds (but) we don't believe there is cholera in the country," Health Minister Qamar Adan Ali told Reuters by telephone from Baidoa in southern Somalia.

The World Health Organisation said in a report this week acute watery diarrhoea has killed 251 people and had infected 5,602 since January.

Aid agencies say there is an epidemic of cholera -- a bacterial disease spread mainly through contaminated water -- in the Horn of Africa nation. Late last year, Somalia was ravaged by the worst flooding in decades.

"There has been a continued increase in cholera cases reported in and around Mogadishu. Over two hundred cases have been reported by one hospital," said David Gilmour, Somalia country director for aid agency CARE International.

"More worryingly, until there is unrestricted humanitarian access across Somalia it is difficult to know the true scale of this and other problems which are going unreported," he said.

Insecurity after a war between Islamists and government troops backed by Ethiopian armour has made humanitarian missions all but impossible -- never the easiest work in a nation in anarchy since a 1991 coup ended central rule.

Floods, insecurity and war-damaged infrastructure combine to raise the risk of cholera in Africa. The disease has infected some 12,000 people already in 2007, mainly in a belt spreading from Angola to Congo.

(Additional reporting by Sahal Abdulle in Mogadishu)

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