Doctors Without Borders (MSF) said that it was pulling its non-local staff from an eastern region of Democratic Republic of Congo after it said an armed group tried to enter its compound.
The NGO becomes the latest aid agency to withdraw its staff from the Biakato region after an unclaimed attack last week saw three Ebola workers killed at an accommodation camp in Biakato Mines in Ituri province, causing the World Health Organization to withdraw its staff from the area.
MSF and an Ebola Treatment Centre (ETC), which is treating two people with confirmed cases of Ebola and nine suspected cases, decided to stay in the Biakato region despite last week's incident.
The NGO said that on Tuesday night a group wielding machetes and sticks broke into the Biakato Health Centre, which houses the ETC, but did not cause any casualties and did not enter the Ebola facility.
A separate group with the same weapons then tried but failed to enter the MSF facility in Biakato Mines.
The NGO said they threw stones but did not do any damage.
"Due to a deterioration in the security situation, MSF made the difficult decision to withdraw all non-local staff from the Biakato region," MSF said in a statement.
According to local authorities, the attackers from last week's incident are likely to be members of the Mayi-Mayi militia group.
The Democratic Republic of Congo is undergoing its 10th Ebola epidemic, which is the second deadliest on record.
An outbreak of the much-feared haemorrhagic virus has killed 2,206 people mainly in North Kivu and neighbouring Ituri, according to the latest official figures.
Insecurity has complicated the epidemic from the outset, compounding resistance within communities to preventive measures, care facilities and safe burials.
On November 4, the authorities said more than 300 attacks on Ebola health workers had been recorded since the start of the year, leaving six dead and 70 wounded, some of them patients.
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