Kenya Protests Erupt as US Military Defies Court Order on Ebola Quarantine Base

Thousands of Kenyans took to the streets of Nairobi on Monday after the US military refused to comply with a court order to halt construction of an Ebola quarantine facility at a key regional base. The standoff has escalated into a diplomatic crisis with Washington, with residents in Mombasa and surrounding coastal regions caught in the middle of a dispute neither government appears willing to back down from. Kenya's High Court issued an injunction last week ordering the US Africa Command (AFRICOM) to stop earthworks at the facility, which local officials say was approved without proper environmental or community consultation.

What the Court Order Actually Said

The order, obtained by Reuters, reveals that Kenyan authorities discovered the US military had begun clearing land for the quarantine unit without submitting the required impact assessments. The court found that AFRICOM violated a 2019 bilateral agreement governing the status of US personnel in Kenya. Judge Grace Wambui, who issued the injunction, gave the US military 72 hours to comply — a deadline that passed without action. State Department officials have since argued the facility falls under "security exemptions" in the agreement, a position Kenya's Attorney General described as "legally untenable." The dispute has now moved to Kenya's Court of Appeal, where judges are expected to hear arguments by Thursday.

Local communities near the base say they learned about the project only when bulldozers arrived. "No one told us anything," said Amina Omar, a trader from Mombasa whose shop sits 800 metres from the construction site. "Now they want to put people with Ebola next to our homes." Environmental groups have filed separate petitions arguing the site sits near a water table that supplies 40,000 residents.

The US Military's Position

AFRICOM's spokesperson, Colonel James Barnett, said the quarantine facility was "essential to regional health security and protecting US personnel deployed to Kenya." The command declined to specify the facility's capacity or cost but confirmed it was part of a broader $32 million infrastructure upgrade at the base, funded through the US Department of Defense. The US embassy in Nairobi said it was "engaging with Kenyan counterparts" but has not acknowledged the court order publicly. US officials, speaking on condition of anonymity, told Reuters the facility was planned in 2022 following an outbreak of Sudan Ebola virus in Uganda that killed 55 people.

The standoff has exposed gaps in how the two countries handle disputes over US basing rights. Kenya hosts roughly 1,500 American military personnel across several facilities, primarily involved in counterterrorism operations in Somalia. Under the 2019 agreement, the US is permitted to operate bases but must coordinate infrastructure projects with Kenyan ministries. The quarantine facility was never submitted for Kenyan review, according to records from the Ministry of Defence.

Regional Health Context

The Ebola angle adds urgency. The World Health Organization reported three confirmed cases of Sudan Ebola in Uganda in January, though the outbreak was contained within six weeks. Public health officials say the risk of spread into Kenya remains low, but the US facility's stated purpose is to quarantine personnel returning from outbreak zones. Dr. Mercy Ndegwa, Kenya's head of disease surveillance, told reporters the government had its own quarantine protocols and "no foreign facility was required." Kenya's Health Ministry confirmed it has quarantine capacity for 200 people across three facilities, all of which were built after a 2014 Ebola outbreak killed 11 people in Kenya.

How Kenyans Are Responding

Protest organisers in Nairobi called for a demonstration outside the Attorney General's office, arguing the government had failed to protect Kenyan sovereignty. "We did not vote for American soldiers to build prisons for our people without asking us," said activist David Mwangi, who helped coordinate the rally. Police deployed water cannon after crowds grew to an estimated 5,000 people, but no injuries were reported. In Mombasa, smaller demonstrations shut down a main road near the base for three hours. Business owners said the protests were disrupting trade ahead of the coastal tourism season, which typically draws 200,000 visitors in December.

What Comes Next

Kenya's Court of Appeal is scheduled to hear the government's challenge to the US military's position by Thursday. A ruling in favour of Kenya could force a full halt to construction and potentially trigger renegotiation of the basing agreement — a prospect US officials have warned would affect intelligence-sharing on Somalia. For ordinary Kenyans near the base, the immediate concern is simpler: whether their government or a foreign military will decide what gets built in their neighbourhood. The appeal court's decision will determine that answer — and may set a precedent for how future US basing disputes are resolved in the region.