Residents and local leaders vowed to continue opposing the facility, arguing that it poses risks to public safety, tourism and local livelihoods. Demonstrators also accused the government of ignoring community concerns and a court order suspending the project.
The Ebola facility is located at Laikipia Air Base, about 8 kilometres (5 miles) from Nanyuki, which lies roughly 200 kilometres (124 miles) north of Nairobi.
The latest unrest comes despite a High Court order suspending the facility and directing the government to disclose agreements underpinning the project.
The US Embassy in Kenya has previously sought to reassure residents, saying the bio-isolation facility poses no danger to nearby communities and forms part of broader efforts to contain the Ebola outbreak in the region.
Police and protest organisers have previously confirmed two people were killed during earlier demonstrations linked to the facility.
