The agency said it was deploying around 30 experts to Mbandaka "to conduct surveillance in the city".
The European Commission said it would dispatch urgent humanitarian aid to contain an outbreak of the Ebola virus in the Democratic Republic of Congo (DRC).
It said the new death has epidemiologic ties to another case.
The reassessment came after the first confirmed case in Mbandaka, a city of around 1.5 million on the banks of the Congo River in the northwest of the country.
It also followed the announcement by Congo's health ministry of 11 newly confirmed cases in the smaller town of Bikoro, near the northwest village where the virus was first detected.
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 center located on major national and global river, road and domestic air routes".
Meanwhile, the public relations officer in the same ministry, Doreen Motshegwa, said their health officials are on high alert and have put measures in place to ward off the spread of the Ebola outbreak in the DRC.
DRC now faces a "very high" risk, the World Health Organization said, after the disease was confirmed in one patient in a major city - raising the assessment from "high" previously.
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The WHO revised its assessment of the risk of spread of the epidemic to "very high" at the national level and "high" for neighboring countries.
The government statement said the total number of Ebola cases is now 45, including 10 suspected cases, 21 probable cases and 14 confirmed cases.
"What we're saying though is that urban Ebola is a very different phenomenon to rural Ebola because we know that people in urban areas can have far more contacts, so that means that urban Ebola can result in an exponential increase in cases in a way that rural Ebola struggles to do".
Mbandaka had three suspected cases in addition to the confirmed case.
Doctors Without Borders said 514 people believed to have been in contact with infected people were being monitored. Under the supervision are already more than five hundred people.
Ebola is thought to be spread over long distances by fruit bats and is often transmitted to humans eating contaminated bushmeat - meat from wild animals such as monkeys or antelopes.
Symptoms include fever, diarrhea, muscle pain and at times internal and external bleeding.
The DRC is at its ninth Ebola outbreak since 1976. The virus can be fatal in up to 90% of cases, depending on the strain.