The WHO is anxious about the disease reaching the city of Mbandaka with a population of about 1 million people, which would make the outbreak far harder to tackle.
The Democratic Republic of Congo warned late on Wednesday that the nation's Ebola outbreak had entered a "new phase" after a case was discovered in the northwestern city of Mbandaka.
The worst-ever Ebola outbreak started in December 2013 in southern Guinea before spreading to neighbouring west African countries Liberia and Sierra Leone, killing more than 11,300 people out of almost 29,000 registered cases.
They stated that this would make the outbreak harder to tackle.
The announcement came just as thousands of doses of the experimental Ebola vaccine arrived in the country, with vaccinations expected to commence this coming weekend.
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The city is a major transportation hub with routes to the capital Kinshasa, the BBC reports.
Senior World Health Organization (WHO) official, Peter Salama, said the spread to Mbandaka meant there was the potential for an "explosive increase" in cases.
Forty-four cases have been reported in the outbreak so far, including 3 confirmed, 20 probable and 21 suspected, according to the WHO's tally. The health body also sent 300 body bags for safe burials in affected communities.
At present, 514 people who may have been in contact with infected people have been notified by the national health authorities and are now being monitored in Mbandaka and Bikoro.
Out of the 20 persons died in DRC, 3 are health workers, Director of the Center John Nkengasong said.