The school is in Shymkent in southern Kazakhstan.
School doctors were the first to hear about the children's HIV status during a BCG vaccination campaign.
The girls' parents wrote to explain why their children should not be vaccinated.
Violating the law on patient confidentiality, the doctors reported this to the school principal. The parents were given 10 days to take their children out of the school.
A local charity, Protect Children From AIDS, has lodged an appeal with the authorities and prosecutor's office.
In 2006, a scandal broke when it was revealed that 118 children and 14 mothers were infected with HIV while being treated at Shymkent hospitals.
It is thought that contaminated blood and medical staff re-using disposable equipment were to blame. In 2007, the doctors involved were found guilty of negligence and sentenced to up to eight years behind bars.
Moscow: A private school in Kazakhstan has expelled two girl pupils who were found to be HIV-positive, local TV outlets reported.
First Published: Saturday, October 06, 2012, 12:20