Four residents were injured in the clashes that flared in Monrovia's West Point slum which has been contained as part of new security measures aimed at containing the deadly virus.
The crackdown in Liberia comes as authorities around the world scramble to stem the worst-ever outbreak of Ebola, which has killed more than 1,200 people across West Africa this year.
Liberian President Ellen Johnson Sirleaf quarantined West Point and Dolo Town, to the east of the capital, and imposed a night-time curfew as part of new drastic measures to fight the disease.
Residents of West Point, where club-wielding youths stormed an Ebola medical facility on Saturday, reacted with fury to the crackdown, hurling stones and shouting at the security forces.
"It is inhumane," resident Patrick Wesseh told AFP by telephone.
"They can't suddenly lock us up without any warning, how are our children going to eat?"
Liberia, with 466 deaths from 834 diagnosed cases, has seen the biggest toll among the four West African countries that have been hit by Ebola.
Deaths from the epidemic that has swept through West Africa since March now stand at 1,229 after a surge of 84 victims in just three days, according to the World Health Organization (WHO).
Fears that the virus could spread to other continents have seen flights to the region cancelled, and authorities around the world adopting measures to screen travellers arriving from affected nations.
Late on Wednesday Vietnam said it had released two Nigerian air travellers from isolation after their fevers subsided. In Myanmar a local man is still undergoing tests after arriving from Guinea with a fever.
From its initial outbreak in Guinea -- where 394 people have died so far -- the virus spread to Liberia, Sierra Leone and Nigeria, overwhelming inadequate public health services already battling common deadly diseases such as malaria.
Straining the situation even further, several top officials leading the fight have lost their lives to the disease.
A doctor who treated Nigeria's first Ebola patient was named among the dead on Tuesday, taking the death toll in Africa's most populous country to five.
Health Minister Onyebuchi Chukwu said the doctor was "the most senior who participated in the management of the (first Ebola) patient," Liberian-American Patrick Sawyer, 40.
The UN's new point man on Ebola, David Nabarro is due Thursday to begin a visit to West Africa aimed at shoring up health services in the four affected nations.
The British physician said he would focus on "revitalising the health sectors" in the affected countries, many of which have only recently emerged from years of devastating conflict.
Efforts to contain the epidemic have also run up against local distrust of outside doctors, and stories of aid workers carrying the infection.
Liberia's leader warned that local rituals were among the factors spreading the disease.
"We have been unable to control the spread due to continued denials, cultural burying practices, disregard for the advice of health workers and disrespect for the warnings by the government," Sirleaf said.
WHO spokesperson Fadela Chaib noted "encouraging signs" in Nigeria and Guinea, where prevention measures and work to trace lines of infection were starting to take effect.
The Nigerian outbreak has been traced to a sole foreigner, a Liberian-American who died in late July in Lagos. All subsequent Nigerian victims have had direct contact with him.
In Sierra Leone, where 365 people have died from the virus, the outbreak has also been traced back to one person: a herbalist in the remote eastern border village of Sokoma.
"She was claiming to have powers to heal Ebola. Cases from Guinea were crossing into Sierra Leone for treatment," Mohamed Vandi, the top medical official in the hard-hit district of Kenema, told AFP.
No cure or vaccine is currently available for Ebola, which is spread by close contact with body fluids, meaning patients must be isolated.
Given the extent of the crisis, the WHO has authorised largely untested treatments -- including ZMapp and the Canadian-made VSV-EBOV vaccine, whose possible side effects on humans are not known.
Three doctors in Liberia who had been given the experimental US-made ZMapp are reportedly responding to the treatment.
Countries throughout Africa and beyond remain on high alert, however, with the Equatorial Guinea airline, Ceiba Intercontinental, the latest to suspend flights to the whole region.
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