Emergency funding to help hundreds of thousands of refugees in Uganda will run out next month unless more support comes in, a United Nations agency said on Monday.

A funding crisis is threatening programmes for people fleeing from strife-torn countries in the region, including Sudan, and Uganda's neighbours, South Sudan and the Democratic Republic of Congo, the UN refugee agency UNHCR said.

"Emergency funding runs out in September," Dominique Hyde, the agency's Director for External Relations, said in a statement.

"More children will die of malnutrition, more girls will fall victim to sexual violence, and families will be left without shelter or protection unless the world steps up."

UNHCR and other UN agencies face one of the worst funding crises in decades, compounded by U.S. and other donor states' decisions to slash foreign aid funding.

Uganda is home to 1.93 million refugees, more than a million of them under 18, according to UNHCR figures.

An average 600 people are still coming in every day and the overall figure, already the largest in Africa, is due to rise to 2 million by the end of the year, the agency says.

It said it would only be able to meet a third of the costs associated with supporting Sudanese refugees in Uganda, and would have to cut its monthly funding to $5 per refugee from $16 unless more money is found.

Malnutrition rates are rising as food, water, and medicine supplies shrink, while the risk of suicide is increasing among young refugees due to a reduction in mental health staff, the agency added.