Officials said 724 patients were currently hospitalized.
The first Americans affected by the policy are 7 aid workers who had been responding to the DR Congo outbreak.
Fifteen countries have strict restrictions on traveling to and from Uganda, including the US.
More than 750 have died from Ebola in the past 2 months.
The antiviral would be given as post-exposure prevention.
A second American has contracted Ebola in the Democratic Republic of the Congo, and the death count has now topped 700.
A WHO official warns the outbreak could be 2 to 4 times larger than the number of confirmed cases, which are now around 1,800.
Acting CDC Director Jay Bhattacharya addressed CDC staff in an internal email on outbreak response.
The strike, over poor pay and scant supplies, could hamstring a clinical trial of potential therapies.
The first patient was randomized today in a clinical trial to see whether 2 antiviral therapies can improve survival in people with Bundibugyo virus.
