Eight samples were taken from Djera, located in the Boende region of Congo's northwest Equateur province, and two of them came back positive, Felix Kabange Numbi said on state television Sunday.
Congolese officials believe Ebola has killed 13 people in the region, including five health workers, Kabange said.
He said 11 people were sick and in isolation and that 80 contacts were being traced.
"This epidemic has nothing to do with the one in West Africa," Kabange said.
This is the seventh outbreak of Ebola in Congo. The disease was first discovered there in 1976.
"The experience acquired during the six previous epidemics of Ebola will contribute to the containing of this illness," Kabange said.
Boende is the region where the World Health Organization said an outbreak of hemorrhagic gastroenteritis has killed 70 people in recent weeks.
The WHO said last week those deaths were not Ebola-related, but WHO spokesman Gregory Hartl said by email Sunday that the information was the result of "miscommunication from the field."
Hartl said on Twitter that samples tested at a national laboratory were positive for Ebola and that the results of confirmation tests from a laboratory in Gabon would likely come back Monday.
He said it was possible the outbreak could be unrelated to the outbreak in West Africa, where a total of 2,615 infections and 1,427 deaths have been recorded in four countries -- Liberia, Guinea, Sierra Leone and Nigeria.
Djera, a collection of villages, is more than 1,200 kilometers (745 miles) from Congo's capital, Kinshasa. It is more than 600 kilometers from the provincial capital, Mbandaka.
Kabange said Djera would be placed under quarantine.