At least 45 people have died out of at least 2,576 cases recorded since July in 12 of the country's 18 states, according to a health ministry report this week seen by Reuters.
"What we see in the health facilities is the severe cases of dengue, which means that what we are seeing is just the tip of the iceberg," Dr Nima Abed, World Health Organization representative in Sudan, said.
Most people do not go to the doctor because the symptoms are not severe enough or they don't realise they have dengue fever, he added.
Although dengue fever is endemic in Sudan, outbreaks were previously concentrated in peripheral provinces, and had not spread through the country.
With help from the United Nations and charities, the health ministry has been able to provide diagnostic tests, mosquito nets and care facilities to help counter dengue infections, ministry official Dr Leila Hamadelnil said.
But Abed said such funds could run out.
"I cannot say it is sufficiently funded to contain the outbreak everywhere," Abed said, noting in particular the cost of funding health workers, who have often gone on strike in Sudan.