A mob surrounds the isolation unit in West Point, Monrovia
George Williams, head of the Health Workers Association of Liberia, said the unit housed 29 patients receiving preliminary treatment before being taken to hospital.
It is understood at least 17 of the 29 are at large.
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Gallery: Harrowing Images From Ebola Isolation Wards
A sick man staggers through a makeshift ebola isolation ward in Liberia
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Gallery: Harrowing Images From Ebola Isolation Wards
A sick man staggers through a makeshift ebola isolation ward in Liberia
Health officials say they fear the looting attack at the unit in West Point will spread ebola infections in Monrovia.
The West Point neighbourhood is home to an estimated 60,000 to 100,000 poor Liberians.
Ms Wesseh said she heard the raiders shouting that President Ellen Johnson Sirleaf "is broke", adding: "She wants money. There's no ebola" in Liberia.
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Residents were also angry that patients were brought from other parts of the capital to the holding centre, witnesses said.
Most of the raiders were young men and were armed with clubs. They broke into the isolation unit set up in a high school, Ms Wesseh said. Nurses also fled the attack.
The looting of the centre came as Kenya closed its borders to travellers from Liberia, Guinea and Sierra Leone because of fears about the spread of ebola.
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National carrier Kenya Airways said it was suspending its flights to Monrovia and Freetown from Wednesday.
At least 1,145 people have died across West Africa this year because of the world's worst-ever outbreak of the virus.
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The charity said it could take six months to bring under control.
Ebola is spread by contact with an infected person's bodily fluids, such as sweat and blood, and no cure or vaccine is currently available.
The last days of a victim's life can be grim, with agonising muscular pain, vomiting, diarrhoea and catastrophic haemorrhaging as vital organs break down.