"The use of condoms to prevent the spread of HIV/AIDS is different from their use for birth control," Health Undersecretary Mario Villaverde told a media briefing.
"The church's position is detrimental to public health," he said.
Besides the use of condoms, which have 95 percent effectiveness in preventing HIV/AIDS, the government will also encourage education on the topic and promote measures to guard against the spread of sexually transmitted diseases, the official said.
Villaverde did not say how condoms would be promoted in a country where all forms of artificial contraception are strongly opposed by the church.
Although rates of HIV/AIDS remain low in the Philippines, the level has recently gone up with an average of 29 cases detected each month in 2007 and 2008, compared with 20 cases a month in previous years.