A record 184 people were infected with the human immunodeficiency virus between July and September, according to a health ministry commission monitoring the virus.
The number of newly confirmed HIV cases was the highest on record in terms of a monthly average, officials of the Health, Labor and Welfare Ministry said.
The government started compiling statistics of this kind in 1985.
The previous highest average, recorded under a different method, was 60 per month logged in the May-June period of 1999.
During the three-month period covered by the latest report, 100 new AIDS cases were confirmed and eight people were confirmed to have died, bringing the total number of AIDS deaths in Japan since the disease first surfaced to 1,278.
Sexual contact among males was the most common route of infection for both HIV and AIDS, the officials said, and homosexual contact was a more common infection route for HIV than heterosexual contact.
According to the commission's report, more than 80 percent of people with HIV or AIDS were men. Among the 165 males recorded with HIV, 92 were infected through homosexual contact.
In the previous survey, covering April to June, the number of males infected with HIV through homosexual contact stood at 17, compared with 26 infected through contact with women.
But the latest survey shows 32 men having been infected with HIV through homosexual contact and 25 through heterosexual contact.
Hiroshi Yoshikura, chairman of the commission and head of the National Institute of Infectious Diseases, said that the number of cases in which people contracted AIDS without knowing they were infected with HIV is showing a disturbing increase.
"This is a very big problem," he said.