Rebels believed to belong to the Allied Democratic Forces (ADF) have killed more than 70 civilians in massacres since the Congolese army launched an offensive against them this month.
The police force tweeted a photo of the Beni mayor's office with flames shooting from the window and thick black smoke billowing above.
"Security forces are working to re-establish public order," it said.
Violence by the ADF and a patchwork of militias and criminal bands near Congo's borders with Uganda and Rwanda have regularly killed civilians and hampered efforts to eradicate a more than year-long Ebola outbreak.
The ADF has been operating near the Ugandan border for more than two decades. It is one of dozens of rebel groups active in the mineral-rich areas where civil wars resulted in millions of deaths around the turn of the century.
Last week, suspected ADF militants killed at least 19 people, kidnapped others and torched a Catholic church.
Several ADF attacks have been claimed by Islamic State, but the extent of their relationship remains unclear.
The World Health Organization said last week that while the number of new Ebola cases in the ongoing outbreak, the second deadliest of all time, was down considerably, it was unable to stamp out the epidemic due to insecurity.