The international conservation body, the WWF, has called for urgent action to protect the hippopotamus.
A survey conducted in one of the animals' former strongholds, the Virunga National Park in the Democratic Republic of Congo, found that only 1,300 of the animals remain in the area, a drop of 95% in 30 years.
Hippos have been threatened by civil warfare in the country
The WWF, formerly known as the World Wide Fund for Nature, says the steep decline is due to demand for hippo teeth sold in the illegal global ivory trade.
Wildlife groups have only recently gained access to the park which has suffered from years of interfactional fighting during the country's civil war.
"WWF is concerned that unless trade is closely controlled and poaching is stopped, hippos will be threatened with extinction," said Director of WWF International's species programme Susan Lieberman.
The WWF warned that the devastation of the hippo population had also had a dramatic effect on fish stocks in the area, in turn affecting the livelihoods of local people.
Hundreds of tonnes of vital nutrients from local freshwater ecosystems - such as Lake Edward within the park which supports more than 20,000 people - were being lost daily, it said.
And grass eaten by hippos while grazing helped to maintain grasslands and open up paths for other animals to get to watering holes, it added.
However, the organisation said that a peace deal signed in 2003 and the formation of a transitional government in the country had raised hopes of proper planning and management of the country's natural resources.
Virunga is the oldest park in the Democratic Republic of Congo, and stretches from Lake Albert in the north through Lake Edward to the northern end of Lake Kivu.