Ahmed Bilal Osman told Reuters that outbreaks of bacterial meningitis had already occurred in three areas of Sudan with 340 cases this year and he expected an epidemic to hit the African country by this April or May.
"Every 6-10 years we get an epidemic that moves across the meningitis belt of Africa and ... this year I fear we will have one by April or May," he said in an interview.
Osman said the government had already distributed 2 million vaccinations and had a 24-hour team monitoring the outbreaks.
Meningitis is an infection of the fluid in the spinal cord and fluid that surrounds the brain. Bacterial Meningitis is the more severe form that can result in brain damage and even death.
Osman said meningitis had infected children in Kamlin in central Sudan this week.
He said the government had advised people not to hold large gatherings in infected areas. Bacterial meningitis is passed on by contact with nose or throat discharges from someone infected.
Surveys have shown the war-ravaged south of Sudan has one of the most unique combinations of diseases in the world. There is little infrastructure in the south, and a swamp area the size of France is infested with malaria-carrying mosquitoes.
The government signed a peace deal with rebels in the south to end a civil war that killed 2 million people, mainly by famine and disease, but a separate conflict in west Sudan that has made some 2 million homeless is unresolved.
Osman said the ministry was this week launching a campaign to fight malaria, which affects 7.5 million people every year of the about 30 million people in Sudan.
"This is one of our biggest problems in Sudan ... Economically it costs 40 percent of crops due to farmers' absence because they have malaria," he said.
Sudan's population is mostly agricultural but in recent years oil exports have begun, contributing around 45 percent of the budget.
Osman said the government had begun distributing mosquito nets impregnated with repellent in a bid to protect pregnant women and children.
"We have 1 million nets which we are distributing for free," he said, adding that they would also give out repellent spray and improve education and training of doctors in rural areas to combat the spread of the disease.
"We are also trying to educate people to dry up stagnant puddles of water," he said.
He said a previous campaign in the Khartoum and Gezira states had reduced the percentage of the population with malaria to less than 10 percent from more than 48 percent two years ago.
"This campaign aims to reduce the infection rate of malaria to below 3.5 million people (a year) by next year," he said.