The second-largest Ebola outbreak on record is over after nearly two years and more than 2 200 deaths, Democratic Republic of Congo said on Thursday, even as a separate flare-up of the virus continued on the other side of the country.

Despite effective vaccines and treatments that dramatically boosted survival rates, the outbreak dragged on as first responders struggled to gain access to virus hotspots in Congo's restive east.

"Compared to previous outbreaks, this last one was the longest, the most complex and the deadliest," Health Minister Eteni Longondo told reporters.

Congo has suffered 11 Ebola outbreaks since the virus was discovered near the Ebola River in 1976, more than double any other country.

Its equatorial forests are a natural reservoir for the virus, which causes severe vomiting and diarrhoea and is spread through contact with body fluids.

This outbreak saw 3 463 confirmed and probable cases and 2 277 deaths.

"It wasn’t easy and at times it seemed like mission impossible," said Matshidiso Moeti, the World Health Organization's Africa regional director.

Even as health officials celebrated the end of one Ebola epidemic, they face another, unrelated one more than 1 000 km (620 miles) away in the western city of Mbandaka.

That outbreak, declared on June 1, has seen up to 24 cases so far, including 13 deaths.

Longondo he said he expected the response there to be easier because it is in a more stable part of the country where a previous epidemic in 2018 was quickly controlled.

In eastern Congo, some community leaders and local residents were suspicious of the response because they believed Ebola did not exist or resented being overlooked by donors.

Treatment centres were attacked by militia fighters who are active near Congo's borders with Uganda and Rwanda, and by angry local residents.

The largest Ebola outbreak in history occurred in West Africa from 2013-2016. It killed over 11 300 people mostly in Guinea, Liberia and Sierra Leone.