The infection of a mother and her child brought to 13 the number of people known to have contracted the virus which causes AIDS in the hospital in the Och region, nine of whom are children.
Ministry official Boris Shapiro said an exercise to screen thousands of children who had passed through the hospital since January 2005 would be launched.
President Kurmanbek Bakiyev has already ordered the state prosecutor to open an inquiry into the matter, which first came to light through media reports last month.
"The infections... occurred during injections and blood transfusions," the health ministry said in an earlier statement.
Those sacked were the head doctor of the Nookatsk hospital, 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.
A similar scandal broke out last year in neighbouring Kazakhstan, where some 100 children were infected with the AIDS virus and 21 medical staff were sentenced to prison terms of up to eight years.