World Health Organization deputy director for emergency preparedness Peter Salama said urgent containment measures were needed. The city is about 93 miles from Bikoro, the rural area where the outbreak was announced last week. Twenty-three of those people have died.
Doctors Without Borders, or MSF as its often called by its French acronym, said it too is stepping up its response to stop the spread of the current Ebola outbreak in the Democratic Republic of Congo.
"We expect an increase in the number of cases confirmed in the coming days and weeks, so we are stepping up our intervention efforts because medical teams on the ground will need more support and capacity and increased access to medicines and equipment", health ministry spokeswoman Jessica Ilunga told Al Jazeera.
Mbandaka, in the Democratic Republic of Congo, has a population of about 1.2 million and is a hub for trade and travel in the absence of a functioning road network in the region. It is an hour's plane ride from Kinshasa or a four- to seven-day trip by river barge.
"With the new case confirmed in Mbandaka, the scenario has changed, and it has become more serious and worrying, since the disease is now affecting an urban area", said Henry Gray, MSF emergency coordinator in Mbandaka.
There is no licensed drug to treat or prevent Ebola, although an experimental vaccine arrived in the DRC on Wednesday and has been cleared for use by the Kinshasa government.
That challenge amplifies greatly in urban environments where people move around more and have more contact with others than in the countryside.
Those exposed to the suspected Ebola cases will for the first time in Congo receive Ebola vaccinations, the health minister said.
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.
World Health Organization said it was deploying about 30 experts to conduct surveillance in the city.
The experimental vaccine has been shown to be highly effective against Ebola.
The UN agency has been working with the Ministry of Health and Médecins Sans Frontières to conduct the ring fence vaccinations across the affected areas - where contacts of those infected, followed by contacts of those contacts, would all be vaccinated. The virus initially is transmitted to people from wild animals, including bats and monkeys.
In this photo taken Saturday, May 12, health workers don protective clothing as they prepare to attend to suspected Ebola patients at Bikoro Hospital in Bikoro, Congo.
The average fatality rate among those infected with the virus is about 50 percent, according to the WHO.
Symptoms include fever, vomiting, diarrhea, muscle pain and internal and external bleeding.