Twenty people have already died from haemorrhagic fevers in and around Mangina, a densely populated town about 30 kilometres southwest of the city of Beni and 100km from the Ugandan border, the ministry said in its statement, without saying when the deaths occurred.
"Although we did not expect to face a tenth epidemic so early, the detection of the virus is an indicator of the proper functioning of the surveillance system", said the country's health minister, Oly Ilunga Kalenga, in a statement.
The province, known as North Kivu, is a conflict zone and is home to 1 million displaced people.
He said a mobile team of 12 will be arriving in Beni tomorrow to set up a laboratory.
Ebola is considered endemic to Congo because of its equatorial forest ecosystem.
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A fresh outbreak of Ebola has occurred in the Democratic Republic of the Congo, just days after the country declared itself free of the deadly virus.
"We really need to get into the area to do epidemiological investigations, try to find cases, try to work with health workers, to strengthen infection prevention and control measures and also to start with the contact tracing", he said. Four samples taken from six people who have so far survived tested positive for Ebola, the ministry added.
"This is an active conflict zone", Peter Salama, the World Health Organization deputy director-general for emergency response, said in a statement, calling the region very different from where the last outbreak occurred.
The declaration brought the curtain down on an outbreak which began two months earlier in the remote northwestern area of Bikoro, about 2,000km from Mangina, on May 8 and culminated in 54 confirmed cases of Ebola, 33 of which proved fatal.
Authorities have not yet revealed how many cases have been detected. "The major barrier will be safely accessing the affected population". The province shares borders with Rwanda and Uganda with a great deal of cross border movement due to the trade activities.