The Ministry of Health of the Democratic of the Congo (DRC) informed WHO that four out of six samples tested positive for Ebola virus at the Institut National de Recherche Biomédicale (INRB) in Kinshasa.
Twenty deaths from hemorrhagic fever have also been recorded in the area, the ministry said. Those 54 Ebola cases included 33 deaths.
Worldwide health experts have arrived in the region. "What adds to our confidence in the country's ability to respond is the transparency they have displayed once again".
Julien Paluku, governor of North Kivu province, announced the outbreak on Twitter, just a week after Congolese and United Nations health officials announced the end of a separate outbreak that killed 33 people in the country's northwest.
The latest outbreak comes after DRC authorities declared a previous emergence of the disease - which has no proven cure - over on July 24.More news: Ishant tears through the England batting line-up
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He says it is crucial to gain access to the area as quickly as possible.He says having people and material in the country from the outbreak in Equateur is very helpful in tackling the outbreak.
"We had a vaccine - and that I think is going to be extremely important for the future of Ebola control", Peter Salama, deputy director-general of emergency preparedness and response at the World Health Organization, told CNN of the July outbreak.
The new cases are in Mangina in the eastern Mabalako health zone, about 30 kilometers (18 miles) west of Beni, a city of more than 230,000 people.
Equator Province is located more than 1,500 miles from North Kivu, and there was no indication that the two epidemics were related, according to the health ministry. The province shares borders with Rwanda and Uganda with a great deal of cross border movement due to the trade activities.
Ebola is endemic in the DRC, which now has had 10 outbreaks since the virus first was discovered there in 1976.