"Soldiers are left in the park without being fed nor paid and that's a recipe for disaster," said Marc Languy, who heads WWF's regional program.
Following a five-year war in this central African country, the postwar transitional government has had little success in calming the east, where killings, looting and rapes continue almost unabated.
Conducted last month, the hippopotamus survey was carried out by the Congolese Institute for Conservation of Nature, the European Union and WWF.
The disappearance of hippos also triggers serious secondary effects for the population, the WWF said. Because hippo dung provides vital nutrients for the fish in Lake Edward, its absence has led to a rapid decline of the lake's fish stocks.
"If the government does not take the hippo situation in Virunga seriously, this will not only lead to an environmental disaster, but also to an economic crisis for local communities," said Languy.