The acting director of Health Services Dr Henry Mwebesa on Monday issued a notice directing all district health officers in the country to be vigilant.
In the latest outbreak, declared last week, 43 people are believed to have been infected in North Kivu province, including 33 who have died, the United Nations health agency said.
A health worker prepares an Ebola vaccine to administer to health workers in Mbandaka, Congo.
He said so far, 26 case with haemorrhagic fever signs, including twenty deaths in the area of North Kivu have been reported.
That outbreak more than 2,500 kilometres away had 33 confirmed Ebola deaths.
There are 33 additional "suspected cases" in the North Kivu outbreak that are pending lab test results to "confirm or exclude Ebola virus disease", according to WHO.
More than 3,000 doses remain in stock in the capital Kinshasa, allowing authorities to quickly deploy it to the affected areas near the Ugandan border.
Three healthcare workers have been affected, including two who died, the World Health Organization said.
World Health Organization has warned that this new outbreak poses a particular challenge as the region is a "war zone" with several active armed groups and tens of thousands of displaced people.
At least four Ebola deaths are confirmed in the new outbreak, Health Minister Dr Oly Ilunga Kalenga said in a statement.
"Teams are conducting investigations on the ground to identify the contacts of the confirmed cases, including health workers", he told reporters in the town of Beni.
There is no specific treatment, and the virus can be fatal in up to 90 percent of cases, depending on the strain.