The call came from the National Committee on AIDS Control and private pressure groups. Health groups will meet next month to discuss strategies to halt the spread of the disease, particularly between males.
Same-sex relationships remain a largely taboo subject in Indonesia, where conservative attitudes prevail despite the country's generally tolerant brand of Islam.
And while intravenous drug use has overtaken male-to-male sex in the rapid spread of HIV/AIDS, failure to acknowledge the existence of homosexuality is hampering efforts to raise awareness, said Suharto, a member of the committee.
Health groups will hold a meeting in September exploring ways of getting officials and religious leaders to accept that Indonesia is home not only to gays but also transvestites, bisexuals and heterosexuals with varying homosexual experiences.
"We will also try to address the openness absent in the government and also in religious groups in this matter," Suharto said.
He said the September "Sexuality and Male Sexual Health" conference would try to develop strategies for tackling the male-to-male spread of the disease and make recommendations to the government and other bodies dealing with AIDS.
"This is the first meeting where we will not shun the aspects of religion," said fellow committee member and academic Dede Oetomo.
The World Health Organisation and the United Nations anti-AIDS body UNAIDS have warned that Indonesia is in danger of a major HIV explosion unless urgent action is taken.