Two of the patients later died, while the third returned to the centre in the city of Mbandaka.
This presents a new challenge for health workers battling to stop the spread of the contagious disease, says the BBC’s Anne Soy in DR Congo.
Ebola has no known cure.
Health officials fear it could spread rapidly in Mbandaka, a densely populated city of one million.
Isolation is the main way to keep the disease under control.
The WHO says 58 cases of Ebola have been recorded since the outbreak was declared on 8 May. There have been 27 deaths so far, with three deaths confirmed as Ebola.
How did the patients leave?
The patients’ relatives came to the centre, which is run by medical aid agency Medecins Sans Frontieres (MSF), and demanded to take them for prayers, WHO officer Eugéne Kabambi told the BBC.
They were reportedly taken away on motorbikes and a search was ordered by the police.
One patient was found dead at home and his body was returned to the hospital for a safe burial. The other was sent back to hospital on 22 May and died that evening, according to MSF.