The UN's World Health Organisation also announced that one of its health experts, an epidemiologist, had been infected while working in Sierra Leone.
Also yesterday, Britain's first Ebola patient, a male nurse who also contracted the disease in Sierra Leone, was evacuated to London.
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In Kinshasa, Congolese Health Minister Felix Kabange Numbi said that two of eight samples taken from victims of a mystery fever had tested positive for Ebola.
"The results are positive. The Ebola virus is confirmed in DRC," Kabange told AFP.
Speaking later on public television, he said the confirmation marked the seventh outbreak of Ebola in DR Congo, where the virus was first identified in 1976 near the Ebola River.
But he said the two new cases had 'no link to [the epidemic] raging in West Africa' and were different strains from one another.
Authorities immediately imposed a quarantine around the affected area in Equateur province near Jera, more than 1,200 kilometres (750 miles) northeast of the Congolese capital Kinshasa.
Medical aid group Doctors Without Borders, said it was sending a crew to help handle patients in the area.
The UN's World Health Organisation gave no details of its infected expert but said the person was 'receiving the best care possible'.
Still, the WHO said in a statement, it was considering the 'option of medical evacuation'.
Meanwhile, an isolation ward in a London hospital had been readied for the country's first Ebola patient.
Sierra Leone health ministry spokesman Yahya Tunis hailed the man, a volunteer nurse, as a 'valuable member' of a team which worked with Ebola patients in Kenema, a hard-hit part of the east now under quarantine.
Sierra Leone, where 392 Ebola deaths have been recorded, is one of four West African states struggling to control the spread of the aggressively contagious virus, which can spread through bodily fluids including saliva and blood.
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