Gennady Onishchenko said as much as 0.5% of the country's population aged between 15 and 49 have been registered with the virus 2006. For those between 18 and 24, the figure is 1%.
The top sanitary official said that of the total number of HIV cases, 1,001 are children who caught 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 with HIV/AIDS.
However, the real number of people living with the virus might be approaching one million, Vadim Pokrovsky, the head of Russia's federal AIDS research center and a leading Russian expert on HIV/AIDS, said earlier
Onishchenko also said 16,522 children born from HIV-positive mothers had been under observation before being diagnosed.
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 that 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 leading 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.
Over 29,000 new cases of HIV infection were registered in first 11 months of the year in Russia.