According to aid group Medecins Sans Frontieres (MSF), three patients left of their own accord from the isolation zone of the Wangata hospital in Mbandaka city between Sunday and Tuesday.
Henry Gray, emergency coordinator for MSF said: "One patient had been about to be discharged.
"The two others were helped to leave the hospital by their families in the middle of the night on Monday.
"One of the men died at home and his body was brought back to the hospital for safe burial with the help of the MSF teams; the other was brought back to the hospital yesterday morning and he died during the night."
Hospital staff made every effort to convince the patients and their families not to leave and to continue treatment, Mr Gray said.
It was not immediately clear if the two deaths reported by MSF were confirmed Ebola ones.
As of Thursday, Congo's health ministry reported 31 confirmed Ebola cases, 13 probable ones and eight suspected.
This is Congo's ninth Ebola outbreak since 1976, when the disease was first identified.
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