Kenyan President William Ruto on Thursday said his government was doing "the right thing" by allowing the United States to set up an Ebola quarantine facility in Kenya.

"I can tell you without fear of any contradiction, and I can look at everybody in the eye, ... and tell you we are doing the right thing," Ruto told a press conference during his state visit to South Africa.

"It would be most unfortunate if on one request by the Americans to set up a facility at their cost, we would refuse, we would look very inhuman," Ruto added.

The US government is continuing to build the Ebola quarantine facility at an air force base in Kenya, despite protests and Kenyan court orders blocking it, according to flight data and officials.

At least two people were killed earlier this week in protests in the central Kenyan town of Nanyuki, home to the base where the 50-bed quarantine unit for Americans who might be exposed to the virus is being built.

A Kenyan court first ordered work on the Ebola facility to be suspended on May 28. The US embassy in Nairobi has said it is working with the Kenyan government to resolve any objections.

The Ebola outbreak has infected hundreds in the Democratic Republic of Congo, the epicentre of the outbreak, and has spread to neighbouring Uganda, which has reported 15 cases.