An average of 29 cases a month of the Human Immunodeficiency Virus (HIV) have been reported in 2007 and 2008, compared with 20 cases a month in previous years, he told a news conference.
"Although the Philippines remains a low-prevalence country, it should not be a reason to be complacent as statistics and trends show that the number of those infected are on the rise," Duque said.
A health department report on AIDS in the country called for a focus on "prevention activities geared towards vulnerable populations and a scaled up response for making available affordable treatments and control interventions."
Duque said the main ingredients for a potential AIDS epidemic were present in the Philippines, with condom use among the highest-risk segments of the population of 90 million remaining "below the universal access target."
Just 48 percent of female sex workers, 27 percent of injecting drug users and 49 percent of men having sex with men or who have had sex with multiple partners, used a condom, according to the health department report.
While transmission through heterosexual contact fell to 139 last year from 193 in 2006, transmission from homosexual contact has risen 32 percent to 107 cases over the same period, while bisexual contact nearly tripled to 74 cases, the report said.
A total of 3,305 HIV cases have been reported since 1984 in the Philippines, where 310 people have died from AIDS, the report said.