Kenya’s health minister has told a court he has ordered a halt to preparations for a US-run Ebola quarantine facility, after being held in contempt for ignoring a previous stop-work order.

Many Kenyans strongly oppose the plan and deadly protests have erupted since the facility was announced in May for US citizens evacuated from the Democratic Republic of Congo, which is grappling with a large-scale Ebola outbreak.

It has been constructed at Laikipia air base, about 125 miles (200km) from the capital, Nairobi, with about 50 isolation beds, and was expected to be managed by US medical staff.

Kenya’s government ignored a previous high court order to stop work. Rights groups had petitioned the court, saying the facility was being developed secretly and without consultation. On Monday, the court said it was holding the health minister, Aden Duale, in contempt for failing to respond to the order and he would appear for sentencing.

On Tuesday, Duale apologised to the court, saying he had ordered “the immediate and complete cessation of any intended construction, site preparation, or related activities concerning the Laikipia air base facility pending the hearing and determination of the substantive petition or until further orders of this court”.

Three people have been killed in unrest near the facility.

Kenya has never recorded a case of Ebola and many Kenyans oppose bringing potential carriers of the highly contagious disease into the country. The US has promised $13.5m to support Kenya’s Ebola preparedness efforts, but critics oppose what they see as the colonial overtones of the arrangement.