The group is the latest aid agency to withdraw its staff from the Biakato region, after three health workers treating Ebola were killed in an unclaimed attack last week at an accommodation camp in Biakato Mines in Ituri Province.
That attack prompted the World Health Organization to withdraw its staff from the area, Presstv Reported.
MSF said that on Tuesday night, a group wielding machetes and sticks broke into the Biakato Health Center, where it operates an Ebola Treatment Center. There were no casualties and the group did not enter the Ebola facility, it said.
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 armed militia group, which is fighting for a share of the country's wealth.
The DRC is undergoing its 10th Ebola epidemic, which is the second-deadliest on record.
An outbreak of the much-feared hemorrhagic virus has killed 2,206 people mainly in North Kivu and neighboring 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.