DRC's health ministry has said the new vaccination campaign will target health care providers, contacts of confirmed Ebola cases and their contacts, the same strategy that was used to contain the previous outbreak in Equateur province in which more than 3,300 people were vaccinated.
A Reuters witness on a visit to Mangina, the village in eastern Democratic Republic of Congo where the epidemic was declared, saw health workers in protective suits administering the injections.
"Twelve teams of vaccinators will be deployed in different affected areas", the ministry said, adding that teams had arrived in Beni.
The outbreak declared last week in North Kivu in the northeast near Uganda and Rwanda is a new outbreak and not connected to the one in Congo's northwest that was declared over on July 24, WHO's emergency preparedness chief, Peter Salama, said on Twitter.
On Tuesday, the Ministry also revealed that in total, 43 cases of haemorrhagic fever had been reported in the (Beni) region, including 16 confirmed, 27 probable and 46 suspected cases under investigation.
Nearly 1,000 people who have had "contact" with the virus have been registered in health zones under surveillance, it said. Other residents in Beni and Mangina will receive vaccinations Thursday, authorities said.
Ebola, first identified in the country in 1976, jumps to humans from animals including bats and monkeys.
World Health Organization has said that analysis of genetic sequencing showed it was a separate outbreak from the one 2,500 km (1,500 miles) away in the northwest that ended less than two weeks ago after killing 33 people - but the same Zaire strain.
There is no specific treatment, and the virus can be fatal in up to 90 percent of cases, depending on the strain.