At least 20 people have died after showing symptoms of haemorrhagic fever in and around the village of Mangina, the Congolese health ministry said.
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.
In addition, 12 Ministry of Health experts including epidemiologists and doctors will travel to Beni with a mobile laboratory and protective equipment from the National Institute of Biomedical Research in Kinshasa.
The Ministry of Health noted that therapeutic treatments are still in country from the last outbreak, but the species of this Ebola virus has yet to be determined.
The confirmation of Ebola return to the DRC was earlier reported by Governor Julien Paluku of the North Kivu province.
The World Health Organisation has started moving staff and supplies into the area.
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New Ebola outbreak has been declared in the Democratic Republic of Congo.
The government confirmed to the World Health Organization on Wednesday that four out of six samples tested for Ebola virus at the Institut National de Recherche Biomédicale in Kinshasa returned a positive result.
They head to a region where deep security problems could complicate efforts to contain the virus.
However, the outbreak "is occurring in an environment which is very different from where we were operating in the northwest", a statement quoting Peter Salama, deputy director-general for emergency preparedness and response read.
An outbreak from 2014 to 2016 killed over 11,000 people in Sierra Leone, Liberia and Guinea. The province shares borders with Rwanda and Uganda with a great deal of cross border movement due to the trade activities.
This is the central African country's 10th outbreak since 1976, when the virus was discovered near the eponymous river in the north.
"What adds to our confidence in the country's ability to respond is the transparency they have displayed once again", Tedros added.