The ministry said in a statement the disease killed 58 people and sickened 1,293 others between Thursday and Saturday in Kosti, 420 kilometers (261 miles) south of the capital, Khartoum.
The ministry said it has taken a series of measures to fight the outbreak, including launching a vaccination campaign against cholera in the city, which lies on the west bank of the White Nile River, opposite Rabak, the capital of White Nile province.
The ministry said it also expanded the capacity of an isolation center in cooperation with the United Nations and other international medical groups.
Doctors without Borders said its cholera treatment center in the Kosti hospital has been overwhelmed, prompting health authorities to use adult and pediatric emergency rooms to provide additional space to treat stricken patients.
“The situation is really alarming and is about to get out of control," said Dr. Francis Layoo Ocan, the group's medical coordinator in Kosti. “We’ve run out of space, and we are now admitting patients in an open area and treating them on the floor because there are not enough beds.”
The group said the White Nile River is the most likely source of infection in the city, as many families have been bringing water from it using donkey carts following a major power outage in the area.
Local authorities banned residents from collecting water from the river and reinforced chlorination in the water distribution system, said MSF, the abbreviation for the French name of the group, Medecins Sans Frontieres.
The disease killed more than 600 and sickened over 21,000 others in Sudan between July and October last year, mostly in the country's eastern areas where millions of people displaced by the conflict were located. Another major outbreak in 2017 left at least 700 dead and sickened about 22,000 in less than two months.
Cholera is a highly contagious disease that causes diarrhea leading to severe dehydration and can be fatal if not immediately treated, according to the World Health Organization. It’s transmitted through the ingestion of contaminated food or water.
Sudan was plunged into chaos in April last year when simmering tensions between the military and a powerful paramilitary group, the Rapid Support Forces, exploded into open warfare across the country.
The fighting, which wrecked the capital, Khartoum, and other urban areas has been marked by atrocities including mass rape and ethnically motivated killings. They amount to war crimes and crimes against humanity, especially in the western region of Darfur, according to the United Nations and international rights groups.
The war in Sudan has killed more than 24,000 people and driven over 14 million people — about 30% of the population — from their homes, according to the U.N. An estimated 3.2 million Sudanese have escaped to neighboring countries.