The Horn of Africa has churned out the largest population of Africa’s refugees, largely due to the conflicts in Sudan, South Sudan, Somalia, Ethiopia, and the Democratic Republic of Congo.

The UN Refugee Agency (UNHCR) says the Horn accounts for 67 percent of Africa’s estimated 9 million refugees. Though a burden to host, most of their food, medicine and other basics had, until recently, been in constant supply, thanks to funding from the US and other partners.

Then Washington cut the funding and folded USAID, the largest contributor to the refugee budget. What followed was a struggle to cope. But it has also exposed the region to further security risks.

Kakuma Refugee Camp and Kalobeyei Integrated Settlement in Kenya’s Turkana County, for instance, host 306,000 refugees and dozens of asylum seekers from 25 nationalities.

Gambela in Ethiopia hosts 395,000 refugees in seven camps. Traditionally, aid agencies such as the World Food Programme (WFP), relief agency CARE, and medical charity group MSF (Médecins Sans Frontières/ Doctors Without Borders) helped refugees cope by targeting nutritional needs, giving food rations and helping expectant mothers to deliver safely.

Now, Gambela’s conditions have worsened, aid agencies say, after the aid cuts. This has strained basic services such as food distribution, health care, access to clean water, and sanitation services.

It has forced the suspension of nutrition services in four out of the seven refugee camps at Gambela, leaving around 80,000 children under the age of five at risk of malnutrition, medical charity MSF warned on Wednesday.

It also said disease prevention activities—such as malaria prevention programmes -- have been reduced, exposing thousands in a parasite endemic region.

Aid agencies said they anticipate a rise in malaria cases because the cuts came at the long rains season, which runs from May to October. In July, cases shot up 125 percent from the June numbers. Since January, there has been at least 23,800 cases.

“Cases are expected to rise sharply during this peak transmission period,” said Birhanu Sahile, MSF’s deputy medical coordinator. “This poses a serious threat to already vulnerable refugees who face heightened exposure to malaria-infected mosquitos due to overcrowded living conditions and limited sanitation.”

MSF, which normally did not receive funding from USAID but worked with partners who did, said it would establish a dedicated malaria health post in Tierkidi Refugee Camp—one of the largest, hosting 74,000 refugees. But it said the project would need backup.

“MSF is working at full capacity, but the scale of needs in Kule far exceeds what we can address alone,” Birhanu said. “Without urgent support and interventions from other actors, this crisis will continue to escalate, putting thousands of vulnerable lives at even greater risk.”

The biggest worry for aid agencies, however, is the security risk as refugees continued to be agitated by cut rations and stipend.

Refugees have to make do with as little as 600 calories a day—less than 30 percent of the recommended daily minimum of 2,100 calories per person.

In Kakuma last week, violence erupted as refugees fought over the new “differentiated assistance approach” in aid distribution. It categorises refugees into four groups, based on their individual needs, vulnerabilities, and ability to support themselves.

Five people were injured when violence occurred as refugees rejected the differentiation, arguing that some groups had been placed in wrong groups or omitted. They also raised questions on how people were categorised.

There was also the case of “onward movers” and unregistered asylum seekers whose numbers have been increasing. They are about 10,000 and have been in the camp for more than three years.

There are also 5,000 asylum seekers who have stayed in the camp for more than four years without documentation.

John Kennedy Orache, Turkana West Deputy County Commissioner, told The EastAfrican that funding for humanitarian aid had dwindled, necessitating a new coping mechanism “to prioritise the most vulnerable.”

Last week, rowdy refugees burned down storage tents of the UN World Food Programme (WFP). The agency said the tents were empty at the time.

Officials now fear that such incidents could recur in future as Kenya and partners try to change from encampment to sustainable hosting of refugees under the Shirika Plan. Shirika, to be funded by donors to June 2027 initially, seeks to integrate refugees and asylum seekers into Kenyan society by transforming refugee camps into integrated settlements, while allowing the inhabitants freedom to move around and do business or get a certain category of jobs.

John Burugu, Commissioner for Refugee Affairs in Kenya, said the shift reflects the government's commitment to long-term refugee management.

But those targeted have protested the rationing, and rights watchers have criticised it too.

Human rights activist Joseph Egelan said the new aid system is unfair and discriminatory.

But Kakuma Refugee Camp manager Edward Chebari said categorisation is a key condition for donors.

“The little available resources are not enough for everyone. As a way forward, there are increased sensitisation meetings, enhanced security patrols, increased community engagement meetings and appeals for more support even from private sector," he said.