President Kurmanbek Bakiyev has ordered the state prosecutor to open an inquiry into the matter, which first came to light through media reports on Friday.
"Eleven people have been infected, including nine minors and a medical worker. The infections... occurred during injections and blood transfusions," the health ministry said in a statement.
Those sacked were the head doctor of the Nookatsk hospital in southern Kyrgyzstan, the head of the regional pediatric hospital, the top doctor for the regional diseases centre, and the doctor in charge of the blood transfusion centre.
Two other doctors were reprimanded.