Amid anecdotal evidence of alarm among local people, a doctor at the city's General Hospital, who requested anonymity, told AFP that more than 300 people in Mbandaka had had either direct or indirect contact with Ebola.
Salama said that isolation and rudimentary management facilities had been set up in 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.
"The confirmed case in Mbandaka, a large urban centre located on major national and global river, road and domestic air routes increases the risk of spread within the Democratic Republic of the Congo and to neighbouring countries", the World Health Organization said. The other death was a suspected case in Wangata.
The deployment of this experimental vaccine will prove a major test for not only the efficacy of the vaccine but for global health strategies created to respond to major viral outbreaks such as this. The ministry said no new health professionals had been contaminated.More news: PayPal agrees to buy iZettle for Dollars 2.2 bn
This new case is linked with the epicentre of the epidemic, the east of Lake Tumba. "How are we going to survive if the disease spreads here?"
Until now, the cases and deaths were reported from the rural Bikoro health zone, almost 150 kilometers from Mbandaka, allowing authorities to attempt ring-fencing vaccinations in the the affected areas.
Ebola is notoriously hard to contain, though recent outbreaks in Congo have been managed swiftly by the World Health Organization and Congolese health officials, gaining the government there a reputation as one of the continent's most prepared.
That challenge amplifies greatly in urban environments where people move around more and have more contact with others than in the countryside.
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. Since then, an experimental vaccine has been developed, and 4,000 doses have arrived in the Congo, with thousands more to follow.More news: Skull and Bones delayed until at least April 2019
The WHO is deploying about 30 experts to conduct surveillance in the city and inform local communities on treatment and prevention methods in collaboration with the country's Ministry of Health.
The average fatality rate among those infected with the virus is about 50 percent, according to the WHO.
He said the disease could have been taken there by people who attended the funeral of an Ebola victim in Bikoro, the south of Mbandaka, before travelling to the city.
Still, while using V920 might not be simple, it has the potential to play a major role in preventing this Ebola outbreak from turning out like the one in West Africa just a couple of years back.
This is the ninth Ebola outbreak in Congo since 1976, when the deadly disease was first identified.More news: The dismantling of the North Korea Nuclear site may happen soon
Symptoms include fever, vomiting, diarrhea, muscle pain and internal and external bleeding.