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.
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."