WHO said health workers had identified 430 people who may have had contact with the disease and were working to trace more than 4,000 contacts of Ebola patients who had spread across north-west DR Congo.
The discovery of Ebola in this bustling port city on the River Congo also led World Health Organization to raise its assessment of the regional risk to "high".
It raised its view of the risks after a case of Ebola was confirmed in the city of Mbandaka, which the agency said was "a large urban centre located on major national and worldwide river, road and domestic air routes".
The WHO's International Health Regulations emergency committee will determine on Friday if the current outbreak constitutes a public heath event of international concern.
The health ministry said two new deaths have been tied to the cases, including one in a suburb of Mbandaka. Fourteen cases have been confirmed with laboratory tests.
The emergency meeting is to "consider the global risks" of the deadly Ebola virus disease, which has now moved to an urban area of DRC.
These would be given as a priority to people in Mbandaka who had been in contact with those suspected of carrying the Ebola virus before people in any other affected area, Mr Salama said.
The city of about one million people is a transport hub on the River Congo, prompting fears that the virus could now spread further, threatening the capital Kinshasa and surrounding countries.
"We are entering a new phase of the Ebola outbreak that is now affecting three health zones, including an urban health zone", Ilunga said in a statement.
"WHO and our partners are taking decisive action to stop further spread of the virus", Ghebreyesus added. It's deploying about 30 experts to conduct surveillance in the city and inform local communities on treatment and prevention methods in collaboration with the country's Ministry of Health.
Meanwhile, humanitarian organisation Doctors without Borders has intensified its response to the Ebola outbreak in the Democratic Republic of Congo.
The government statement said the total number of Ebola cases is now 45, including 10 suspected cases, 21 probable cases and 14 confirmed cases.
He said the disease could have been taken there by people who attended the funeral of an Ebola victim in Bikoro, south of Mbandaka, before travelling to the city.
Those exposed will for the first time in Congo receive Ebola vaccinations, the health minister said. Ebola is a highly infectious disease spread through contact with even small amounts of bodily fluid of an infected person.
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