Sexual activity is not a crime but same-sex marriage is not allowed and gay couples cannot adopt children, said the study funded by the UN Development Programme and the US Agency for International Development.
"Cultural and social attitudes towards LGBT (lesbian, gay, bisexual and transgender) people are complex, with signs of acceptance, particularly among the young," the study said.
Several large cities have passed ordinances banning LGBT discrimination, but efforts to pass a national law have foundered amid opposition from the powerful Catholic church, it added.
Hate crimes remained a threat, with 28 killings involving the community tallied in the first half of 2011 alone, it added.
Michael Tan, the author of the study, told a news conference a recent informal survey of 700 Filipino LGBT respondents found one in 10 had been a victim of violence and abuse, mostly committed at home by their parents.
"What we have in the Philippines is tolerance, not acceptance," Manila-based gay rights campaigner Jonas Bagas of the TLF Sensuality, Health and Rights Educators Collective told the meeting.
He said the Filipino LGBT community was "a long way off" the rights enjoyed by their counterparts in many Western countries.
"In many parts of Asia, social and legal environments remain far from inclusive for the LGBT community," UNDP country director Maurice Dewulf said in a speech launching the report.
The UNDP and USAID said they are also collaborating in similar surveys in China, Cambodia, Indonesia, Thailand and Vietnam.
The Philippine report said LGBT people generally suffer discrimination, harassment and abuse at work.
LGBT staff are routinely assigned to night shifts and passed over for promotion "since they don't have families to feed", Tan told the news conference.
Transgender people are not allowed legally to change their identity, first name and sex, while gays can be discharged from the military, and cross-dressers are barred from nightclubs, the report said.
In school LGBT youths suffer from discrimination, bullying and abuse, the report said.