Several Ebola patients, along with individuals showing symptoms of the life-threatening virus, fled the treatment centre in the village of Bafwabango in Ituri province, Joseph Pemamakuwe, the chief medical officer of the local health district, told DPA.
A group of angry young people had sought to block the safe burial of a suspected Ebola victim, despite the family having already given their consent, Pemamakuwe said.
"Everything was burned down," Pemamakuwe said. "Operations have not yet resumed because staff still fear for their safety."
The Ebola virus continues to spread across eastern Congo as mistrust among local communities hampers response efforts.
Aid workers have come under attack amid fear, rumours and superstition surrounding the disease.
Traditional burial practices, which involve close contact with the deceased, remain a major source of transmission.
Since April, at least 438 people have died in the outbreak, according to the latest official figures.
The number of confirmed Ebola cases in the Democratic Republic of Congo increased to 1,406 including 438 deaths, government data showed on Wednesday. The cases were recorded in the eastern provinces of Ituri, North Kivu and South Kivu.
The World Health Organization believes the true number of infections is likely much higher because the outbreak went undetected for several weeks.
Twenty cases have also been confirmed in neighbouring Uganda.
Ebola is a highly lethal disease transmitted through direct contact with infected individuals and their bodily fluids.
The outbreak has hit Ituri province in north-eastern Congo particularly hard. On Monday, authorities announced new measures, including limiting indoor public gatherings to fewer than 50 people.
In neighbouring North Kivu province, which is controlled by rebel forces, authorities banned public gatherings to watch matches involving the Congolese national football team at the World Cup in the US.
with Reuters
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