The two victims were internally displaced people living in the Kpangba camp, which hosts 30,000 internally displaced people, the UNHCR said on Thursday.
As of Friday, Congo had reported 689 confirmed cases and 136 deaths in an outbreak that has also spread to neighbouring Uganda, which has reported 19 cases.
The virus has spread across three provinces since the World Health Organisation declared the outbreak a public health emergency of international concern on May 17.
The affected provinces - Ituri, South Kivu and North Kivu - have been devastated by decades of conflict and are home to more than five million displaced people.
A Congolese health ministry report seen by Reuters showed a 60-year-old woman in the camp tested positive for Ebola on May 30. By then, she had broken out of quarantine and could not be traced by teams, the report said.
She died on May 31 and her daughter died on June 1, an aid worker with knowledge of the cases told Reuters, adding that their bodies had both tested positive for Ebola after their deaths.
Humanitarian workers later discovered the bodies, but community members began pelting WHO vehicles as they tried to approach, the source said.
Mistrust of aid groups has been widespread in the nearly month-long outbreak in Congo, with communities sometimes burying highly-contagious bodies in secret to avoid health protocols.
Aid workers describe cramped conditions at the camps, where sometimes hundreds of people sharing a toilet and open defecation is common.
"We are all really worried that Ebola in these camps will spread extremely quickly and that there will be panic and people will flee all over whether or not they're contacts, whether or not they're ill," Caitlin Brady, country director for the Danish Refugee Council in Congo, told Reuters.
The Congolese health report for the Kpangba camp listed eight contacts for the mother, underscoring the risk of further cases within the camp. The International Organisation for Migration, which provides support there, said it was concerned about further transmission.
"It's a highly populated area so the risks of transmission are obviously higher and worrying," the aid source said.
"These are tents with tarp walls, where do you isolate if you have symptoms?"
At another camp in Ituri province, Kigonze, the chief Desire Grodya Bapi said people had been falling ill and dying but he was not aware of any confirmed Ebola cases.
The outbreak involves the rare Bundibugyo strain of Ebola, for which there is no approved treatment or vaccine. The disease went undetected for weeks and first responders say they are playing catch-up.
