Gennady Onishchenko said, "The discrimination that we have in our society is a very serious obstacle interfering with the objectives we have set."
The disease poses a potentially dire threat for Russia, already under threat from a demographic crisis, as official statistics say a total of 350,000 people are HIV+, but independent experts claim the figure is about three times higher.
Onishechenko, who was speaking after a three-day international conference on HIV/AIDS in Moscow, said more work had to be conducted to prevent the disease from spreading.
"We will do everything possible so that people living with HIV receive access to medicine, but the main task in our work is preventive measures," he said.
Vadim Pokrovsky, head of Russia's federal AIDS research center, said in April that the number of HIV/AIDS infected Russians per 100,000 people was continuing to grow, reaching 225.1 as compared with 200.7 in 2004.
The fight against infectious diseases has been made a priority at a summit of leaders from the Group of Eight industrialized nations in St. Petersburg in July.