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The city was facing a serious shortage of drinking water as the state-owned water board stopped pumping water to households, fearing it could spread cholera, typhoid and other water-borne diseases.
Aminu Umar, the agency's head, told AFP that the flood had damaged vital equipment and contaminated the sources of the water supply for the city, 186 kilometres (116 miles) north of the Nigerian capital Abuja.
A Kaduna state health ministry official on Wednesday warned of a possible outbreak of cholera and other diseases.
Speaking on state-owned Radio Kaduna, Abdulhamid Abubakar also advised people to boil and filter their water before drinking.
Red Cross coordinators say about 1,300 people have been evacuated to temporary camps, out of at least 5,000 left homeless after the Kaduna River burst its banks following days of heavy rain.
Local leaders say the final figure could be much higher.
Most residents of the densely-populated city use water from boreholes and wells for their washing but drink bottled or packaged water, known locally as "pure water". Its true source and purity are, however, unclear.
Kaduna State Governor Ahmed Makarfi said two people were so far known to have died in the disaster, which has destroyed an estimated 30,000 houses in 12 local government districts.
At least eight more people have been killed and 2,215 displaced by flooding in nearby Kano State, where state officials say the disaster has caused millions of dollars' (euros') worth of damage.
Kano relief official Lawal Shehu said the government had already begun distributing emergency aid to flood victims.
The disaster has brought back memories of major flooding in Kano state after heavy rains in 1988, when dozens of people were killed and hundreds of houses destroyed, along with thousands of acres of farmland.
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