Police fired warning shots and tear gas to defuse the incident in Ituri province, which highlighted the struggle that authorities in the Democratic Republic of Congo could face to enforce the safe burials of people with confirmed and suspected cases that are required to help contain the outbreak.
It took place in the town of Rwampara, which has been hit hard by the latest Ebola outbreak caused by the Bundibugyo strain of Ebola, for which there is no approved vaccine or treatment.
Bodies of Ebola victims are highly infectious after death, and unsafe burials - in which family members handle the body without proper protective equipment - are a leading driver of transmission.
The first known case in the outbreak died in Bunia, Ituri's provincial capital, on April 24 and the virus spread after his body was returned home to the nearby town of Mongbwalu and mourners gathered around and touched him during a funeral.
The family of footballer Eli Munongo Wangu on Thursday refused a safe burial for him, disputed that the virus had killed him and demanded to take his body.
Authorities finally buried him overnight into Friday, despite his family's protests.
Munongo had played for several local teams and was a well-known figure in his neighbourhood.
He had been admitted to hospital days earlier.
A doctor told Reuters he was a suspected Ebola case and the hospital had taken samples to run tests.
His mother told Reuters she believed her son had died of typhoid fever, not Ebola.
His family, friends and neighbours gathered outside the hospital to take his body and bury him themselves, against clear instructions that all bodies must be buried safely, said Jean-Claude Mukendi, a senior police officer coordinating security for the response in Ituri.
Soldiers tried to defuse the tension before police intervened, using tear gas and firing warning shots to disperse the crowd, the Reuters witnesses said.
The crowd then set fire to two tents fitted with eight beds run by medical charity ALIMA, Mukendi said, before army and police reinforcements brought the situation under control.
The tents were burnt down, along with a body that was due to be buried that day.
Six patients were receiving treatment in the tents and were being cared for at the hospital, ALIMA said in a statement.
Batakura Zamundu Mugeni, a local customary chief who was present at the scene, said authorities were working with health officials to track down any patients who might have fled as well as contact cases.
Mukendi blamed the unrest on "young people who do not grasp the reality of the disease".
Mistrust and disinformation hampered the response to previous Ebola outbreaks in Congo.
The current outbreak is already the third largest on record, with 160 suspected deaths out of 670 suspected cases, according to DRC health ministry data.
Congo's national football team has been forced to cancel World Cup build-up events in Kinshasa will instead continue preparations in Belgium in order to comply with US travel restrictions.
