The World Health Organisation says three deaths are being linked to the virus, and it is taking the situation “very seriously”.
One of those killed had tested positive for Ebola after coming down with a haemorrhagic fever last month in Bas-Uele, a province which borders the Central African Republic.
WHO spokesman Christian Lindmeier has told Sky News that work is under way to find people who may have been in contact with the Ebola sufferer.
The health agency’s regional director is also on their way to Bas-Uele, where residents are being given advice on how to treat their loved ones and perform safe burials.
Another WHO spokesman, Eric Kabambi, said: “The case is in a very remote zone, very forested, so we are a little lucky.”
The DRC suffered a three-month outbreak of Ebola in 2014. Although it was quickly contained, 49 people were killed.
Ebola occasionally jumps from animals including bats and monkeys to humans – and without preventative measures, the virus can spread quickly between people.
The virus is fatal in up to 90% of cases, and the WHO recently developed an experimental vaccine for use in emergencies.
In a statement, the DRC’s health ministry said: “Our country must confront an outbreak of the Ebola virus that constitutes a public health crisis of international significance.”
Health minister Oly Illunga has urged the population not to panic.
Ebola caused alarm globally in 2013 when the world’s worst outbreak began in West Africa – killing more than 11,300 people and infecting an estimated 28,600 as it swept through Liberia, Guinea and Sierra Leone.
Liberia was only declared free of active Ebola virus transmission last June.
The WHO has warned that the virus could resurface at any time, as it can linger in the eyes, central nervous system and bodily fluids of some survivors.