The World Health Organization says more doses "should be deployed in the coming days".
Health officials have confirmed a case in the northwest city of Mbandaka, a busy river port located at the intersection of the Congo and Ruki rivers and with trade routes to the capital Kinshasa.
The latest outbreak is believed to have killed 23people so far in the country.
M - The Ebola outbreak in Congo has spread from the countryside into a city, prompting fears that the disease will be increasingly hard to control, BBC reported. The Congo Republic is on the other side of the river.
"One new case of Ebola virus disease has been confirmed in Wangata, one of the 3 health zones of Mbandaka, a city of almost 1.2 million people in Equateur Province in northwestern Democratic Republic of the Congo", the UN's health agency said in a statement. He said epidemiologists are working to identify additional contacts to the 500 already identified.
Ebola is most feared for the internal and external bleeding it can cause in victims owing to damage done to blood vessels.
The first batch of over 4,000 Ebola vaccines was sent by the World Health Organization to Kinshasa on Wednesday.
"Five thousand four hundred doses of vaccine arrived from Geneva this morning" said health ministry spokeswoman Jessica Ilunga.
He said the lists of those exposed to suspected Ebola cases would receive, for the first time in Congo, a new component of response to an Ebola outbreak: vaccinations. He said another 4,000-vaccine batch was expected soon.
He said one sample proved positive for the Ebola virus, meaning there have now been three confirmed cases in three different health zones. The health body also sent 300 body bags for safe burials in affected communities.