As an acute cash crunch worsens and with the world's eyes focused on other conflicts such as Syria, another 49 facilities in Sudanese regions are also at risk.
Eleven clinics have already been shut in Darfur, Blue Nile and South Kordofan where years of fighting between government troops and black African rebels has forced tens of thousands of people to flee their homes.
As an acute cash crunch worsens and with the world's eyes focused on other conflicts such as Syria, another 49 facilities in these regions are also at risk, the WHO head in Sudan, Naeema al-Gasseer, told AFP.
"We don't have enough funds to continue supporting clinics in remote areas that provide people with health services," Gasseer said.
"About 11 clinics have already been closed and another 49 are facing closure.
"We are talking about a million people who can be affected."
The closures could impact immunisation services, while some 323,000 women of child-bearing age and children under five will lack access to health care, she said.
"A heightened risk of epidemics is likely... with people having to travel long distances to access available health care services," Gasseer said.
WHO, a United Nations agency, needs about $7 million to operate these clinics over the next year, but is having trouble sourcing the funds.
More than half of these facilities are in Darfur, a vast region the size of France where heavy fighting erupted in 2003.
Violence broke out when ethnic minority rebels rose up against President Omar al-Bashir, accusing his Arab-dominated government of marginalising the region.
Similar fighting has also plagued Blue Nile and South Kordofan, with tens of thousands of people killed or displaced in these three areas in more than a decade.
Funding for Sudan's health care sector has fallen in the past two or three years.
The cash crunch faced by WHO and other NGOs is so severe that many clinics have no money even to buy medicines or to pay staff wages.
"Sudan is like a forgotten emergency," said Adil al-Mahi from Save the Children Sweden, which operates health facilities for children in the conflict zones.
"We don't have funds... to maintain the equipment or for food for malnourished children."
Save the Children Sweden is phasing out health and nutrition services in 20 centres in South Kordofan, affecting about 200,000 people who it has supported.
UN officials insist Sudan still remains a priority for global donors.
The United Nations had launched a global appeal to raise raising $952 million to fund humanitarian needs in Sudan in 2016.
About 55 percent of that has been raised, which UN officials say is significant considering that donors had to meet other massive aid needs in Syria, Iraq, Yemen and Afghanistan.
"International donors have stayed the course over the last five years," said Samantha Newport, spokeswoman for the United Nations Office for the Coordination of Humanitarian Affairs, or OCHA.
"They have donated more than $ 3.2 billion to humanitarian work in Sudan," she said.
But aid allocation to Sudan's health care sector has been meagre, even as the international appeal for the country remains one of the top 10 in terms of funding.
UN officials had estimated $66 million as the requirement for Sudan's health care sector in 2016, but have received only $28 million.
Newport said the bulk of the aid had gone to provide food for vulnerable communities.
"This year, the humanitarian appeal for Sudan has received about $550 million and over $330 million have been to provide food aid to 4.6 million people," she said.
UN officials are now looking for funds from inside Sudan even as the country's economy remains battered by decades of trade sanctions imposed by Washington.
"We can not rely on foreign funding," said UNICEF's head in Sudan, Abdullah Fadil.
UNICEF has spent about $500 million in Sudan over the past five years, he said, but that kind of funding is no longer coming in from international donors.
"So, we have to find different alternatives. That means we have to find resources within Sudan."