Until now, the outbreak was confined to remote rural areas, where Ebola, which is spread by bodily fluids, travels more slowly.
"The Minister of health of the country confirmed case in the city of Mbandaka with a million people in 130 km from the area where it was first recorded cases of the disease this month", - is told in the message.
"The confirmed case in Mbandaka, a large urban center located on major national and worldwide river, road and domestic air routes increases the risk of spread within the Democratic Republic of the Congo and to neighboring countries", the statement said.
The city is about 93 miles from Bikoro, the rural area where the outbreak was announced last week.
She said her ministry would continue to monitor the situation at all levels and will update the public as the epidemic unfolds. Fourteen cases have been confirmed with laboratory tests.
Later on Friday, the WHO will convene an Emergency Committee of experts to advise on the worldwide response to the outbreak, and decide whether it constitutes a "public health emergency of global concern". A newly confirmed case in a densely populated part of the country will complicate attempts to control the outbreak, the statement said.
Mbandaka had three suspected cases in addition to the confirmed case.
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.
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Mr Salama, the WHO's deputy director-general for emergency response, said Mbandaka's location on the River Congo raised the prospect of Ebola spreading to Congo-Brazzaville and the Central African Republic, as well as downstream to Kinshasa, which has a population of 10 million.
"WHO and our partners are taking decisive action to stop further spread of the virus", Ghebreyesus added.
The WHO will be deploying about 30 experts to scrutinise and inspect the city, is working along with the Ministry of Health and also believes in engaging with the communities to prevent and treat and report about new cases.
But WHO advised against any restriction of travel and trade to the Democratic Republic of the Congo based on the now available information.
World Health Organization said it had sent vaccines to respond to the disease and contain it.
WHO-partner, MSF, has also deployed its teams and is working with United Nations agencies to strengthen health capacity to treat Ebola patients.
Notably, about 23 people have reportedly died and 42 people have contracted the virus since Epola outbreak began earlier in May.