The World Health Organisation has sent 5,400 doses of an experimental Ebola vaccine to Congo, with thousands more to be shipped in the coming days.
Adding to concerns is the city's location on the banks of the Congo River, a major thoroughfare for trade and transport into the capital, Kinshasa.
The latest outbreak is believed to have killed 23people so far in the country.
The Democratic Republic of Congo's efforts to head off an Ebola epidemic is running into obstacles, with the announcement of the first registered urban case. The Congo Republic is on the other side of the river.
"Since the announcement of the alert in Mbandaka, our epidemiologists are working in the field with community relays to identify people who have been in contact with suspected cases", he said.
Authorities said they were tracing all air, river, and road routes in and out of the city to find the source of the virus.
This is the ninth Ebola outbreak in Congo since 1976.
Ebola is most feared for the internal and external bleeding it can cause in victims owing to damage done to blood vessels.
"Five thousand four hundred doses of vaccine arrived from Geneva this morning" said health ministry spokeswoman Jessica Ilunga.
Ilunga says the ministry has recorded 42 cases of hemorrhagic fever in Congo's remote northwest. While none has been connected to the one in West Africa, the experimental vaccine is thought to be effective against the Zaire strain of Ebola found in Congo.
He said one sample proved positive for the deadly Ebola virus, bringing to three the number of confirmed Ebola cases in three health zones.
Out of the 20 persons died in DRC, 3 are health workers, Director of the Center John Nkengasong said.