Gennady Onishchenko said 1,059 HIV-positive children contracted the virus from their mothers around the time of birth.
According to official statistics as of the beginning of the year, 346,123 Russians were registered as infected with HIV/AIDS.
However, the real number of infections might be approaching one million, according to Vadim Pokrovsky, head of Russia's federal AIDS research center and a leading Russian expert on HIV/AIDS.
Onishchenko also said 15,828 children born from HIV-positive mothers had been under observation before being diagnosed.
"There is an acute problem in the infection's vertical transmission. Medics can, by way of preventive treatment, ensure that infected mothers give birth to uninfected children," the sanitary chief.
The official also said the virus was increasingly being transmitted by sexual intercourse.
The Russian government has increased spending on HIV control measures by 20 times this year, in an effort to provide treatment for at least 15,000 Russians living with the virus, and to ensure more patients have access to anti-retroviral drugs.
Russia put the issue at the top of its agenda for the first half of 2006 when it took up the presidency of the Group of Eight major industrialized nations.
In the run-up to World AIDS Day on December 1, Onishchenko instructed sanitary regional branches to step up their campaigns to raise public HIV/AIDS awareness, and to explain the objectives behind the government's new nationwide project to curb the pandemic.
