The victims died of Ebola in 200 people in the Congo Peninsula.
Congo's national health authority said the vaccination program has so far delivered 25,000 vaccinations. However, Oly Ilunga, the health minister, said armed insurgents continue to interfere with the medical team.
In September, immunization was stopped at Benny when the rebels launched attacks for several hours. The Democratic Republic of the Congo has been in conflict over years of civil war and political turmoil.
The current Ebola outbreak, which began in July, is the tenth time since 1976 that it attacked the country. Ebola virus spreads through a small amount of fluids and infection is often fatal.
According to a recent report, the Ministry of Health said 291 cases were identified and 201 deaths were recorded. UN peacekeepers have asked the armed groups not to stop health workers from fighting this disease.
Ilunga faced Friday's team "Repeated Destruction of Threats, Physical Attacks, Equipment and Abductions".
"Two of our colleagues in the Rapid Response Medical Unit lost their lives in the attack."
Last week, the World Health Organization (WHO) Secretary General Tedros Adhanom Ghebreyesus said the lack of security was the biggest challenge in fighting the current Ebola epidemic. [BBC/U-5]