In its court petition in May to stop the construction, rights group the Katiba Institute warned that the arrangement posed “grave and imminent risks” to public health.
But in court, Duale dismissed such fears saying any decision he made as the minister of health was “based on science, technical advice and strategic interventions”.
“The fear that the… facility could serve as a vehicle for Ebola importation into surrounding communities is scientifically unfounded.
“The facility is located at a military airbase placing it at a significant geographical distance from populated areas with very strict access protocols,” the minister added.
The health ministry had earlier insisted it had not flouted last month’s court order to stop the joint US-Kenyan building works, because any ongoing construction was being done solely by the Kenyan government in the national interest to protect Kenyans against Ebola.
But on Monday the judge said the government could not “avoid compliance by recasting or re-characterising the ongoing construction”, adding that a court order “is not an invitation to ingenuity – it is a command to be obeyed”.
The judge added that Duale knew and understood that all construction at the Nanyuki site had to stop – yet he allowed it to continue.
In recent weeks Kenya’s President William Ruto has defended the plan for the US-funded Ebola quarantine site, saying he had received a request from the US to establish the centre and a refusal would be “inhuman”.
He also called on Kenyans not to politicise a matter “so serious” as Ebola, asking politicians to avoid “reckless” talk about it.
Kenya, East Africa’s largest economy, had not recorded any Ebola cases as of Monday.
The affected countries are, external the Democratic Republic of Congo, which has recorded more than 1,000 confirmed cases and Uganda which has had 20 confirmed cases – most imported from DR Congo – so far.
The US plan has led to vocal opposition from one of the biggest medical unions in Kenya – the KMPDU – which questioned why the country was chosen to host a quarantine facility for exposed American citizens.
The Congolese city of Bunia, the epicentre of the outbreak, is 780km (485 miles) from Nanyuki, with Uganda separating DR Congo and Kenya.
Davji Bhimji Atellah, KMPDU’s secretary general, said the union “will not sit back and watch Kenya be treated as a containment colony for a lethal pathogen that we did not generate”.
Washington intends to provide $13.5m (£10.7m) in aid to fund Kenya’s Ebola preparedness efforts, according to a spokesperson for US Secretary of State Marco Rubio
That amount is part of a larger $112m US commitment for the regional response to the outbreak.
