Lack of funding has hampered reception of refugees and the quality of protection offered by host countries, the United Nations High Commissioner for Refugees (UNHCR) has said.
Only 12 per cent of the $429 million needed to meet the needs of Burundian refugees across the region had been received by August, according to UNHCR.
In Rwanda, which hosts 87,493 Burundian refugees -- the second largest host after Tanzania -- only 16 per cent of the $82.9 million needed for 2017 has been remitted.
"Refugees continue to live in overcrowded and congested camps, facing insecurity, deterioration of emergency shelters, shortages of water and food, and oversubscribed health and education services," said Catherine Wiesner, UNHCR's regional refugee co-ordinator for Burundi.
"Many refugee hosting areas are at risk of communicable diseases, including, malaria and acute diarrhoea. Because we keep on receiving new arrivals that means the needs are increasing every day."
In Mahama, the largest refugee camp in Rwanda, the impact of the huge gap in funding is evident as UNHCR struggles to meet minimum standards for refugees.
The funding challenge has been linked to the rise of massive displacement in other countries in sub-Saharan Africa such as Somalia, Eritrea, Sudan and South Sudan.
Martina Pomeroy, the external relations officer of UNHCR Rwanda, told The EastAfrican that a quarter of the refugees in Rwanda live under plastic sheeting in overcrowded hangars.
"We are struggling to meet even the most basic needs of refugees such as ensuring adequate shelter, enough water for drinking and hygiene, basic sanitation, and other life-saving needs," she said.