The two new zones affected are Biena and Manguredjipa in Congo's North Kivu province, where the case fatality rate is much higher than the overall rate of 48 per cent, due in part to delayed response efforts, according to health ministry data released on Friday.
It said the outbreak has recorded 5794 confirmed cases, including 2786 deaths, as it is spreading at an unprecedented speed, faster than efforts to track and slow it.
The outbreak in the Democratic Republic of the Congo is spreading under extremely difficult conditions, fuelled by insecurity, displacement, a health workers' strike and intense population movements.
The World Health Organisation has said it remains out of control and is on track to surpass the 2014-16 West Africa Ebola outbreak, the deadliest on record, which killed more than 11,000 people, primarily in Guinea, Liberia and Sierra Leone.
On Thursday, Congo began vaccinating health workers and other front-line workers with the Ervebo vaccine that was effective in past Ebola outbreaks caused by a different, more common type called Zaire.
Clinical trials are on the way find a licensed vaccine for the rare Bundibugyo virus that is causing the current outbreak and which has no approved vaccines or treatments.
Although the current outbreak was declared in mid-May, officials believe it had been spreading since February.
It has spread from three health zones to nearly 60, with most cases and deaths occurring outside the network of monitored contacts and within communities.
Efforts to bring the outbreak under control - from limited public gatherings to social distancing and airport closures - have disrupted life in the six affected provinces, particularly Ituri, which has been ravaged by rebel violence.
The government has introduced measures, including installing health and sanitary equipment at some locations, but advocacy groups say more needs to be done to build trust within the community.