The staff are protesting about the government's failure to pay an agreed weekly $100 (£63) "hazard payment". A few are still assisting at the clinic.
The clinic, in Bandajuma near Bo, is the only Ebola treatment centre in southern Sierra Leone.
In Mali, a nurse and a patient became the second and third people thought to have died from Ebola there.
Nearly 5,000 people have been killed in the outbreak of Ebola in West Africa, mostly in Guinea, Liberia and Sierra Leone.
The World Health Organization (WHO) has declared the outbreak a global health emergency.
The Bandajuma clinic is run by medical charity MSF, which said it would be forced to close the facility if the strike continued.
MSF's emergency co-ordinator in Sierra Leone, Ewald Stars, told the BBC that about 60 patients had been left unattended because of the strike at the clinic in Bandajuma.
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