Same-sex couples will be offered specialised relationship assistance often denied to them, as part of a new program developed by University of Queensland and Latrobe University.

Rainbow Couple CARE is available free to same-sex couples living in Brisbane and Melbourne and covers topics including having a fulfilling sex life and improving communication.

UQ School of Psychology's Professor Kim Halford said most relationship guidance was offered by religious organisations that often "ignore or even reject" same-sex couples.

"Aside from needing legal recognition of their marriage, same-sex couples also need access to good relationship enhancement," Professor Halford said.

Rainbow Couple CARE has been adapted from the Couple CARE program to cater specifically for same-sex couples.

"The program helps currently satisfied couples to strengthen their relationship," Professor Halford said.

"We explore relationship expectations, enhancing communication, promoting fun and mutual support, and having a fulfilling sex life."

He said Couple CARE and Rainbow Couple CARE shared many strategies for building healthy relationships, but there were distinctive challenges gay couples faced.

"Sadly, same-sex couples often have to deal with homophobia, but in our program we explore the experiences related to that and how couples can support each other to sustain a positive gay identity."

Not all religious relationship services reject gay couples

Catholic agency Centacare offers its services to the entire community "regardless of religion, circumstance, ethnicity, economic situation, age, gender or ability", its website says.

Spokeswoman Karyn Kelly told the ABC that same-sex couples are not be denied its counselling services.

"We don't have an exclusive program for same-sex couples, they just become part of regular relationship guidance programs that we offer," she said.

A spokeswoman for Anglicare told the ABC it did not offer relationship counselling tailored for same-sex couples but was "not in the business or turning away anybody".

Tensions between some churches and same-sex unions remain, with conservative elements within Australia's Anglican Church wanting new laws giving Christians the right to discriminate against gay couples.

La Trobe University researcher Timothy Jones wrote for The Conversation in June that LGBTI people are discriminated from a range of social services, including exclusion from some religious schools.

"Over the past 60 years, in particular, religious institutions have come to provide a very large proportion of Australia's social services," Dr Jones said.

"Setting sexual and gender identity rights against religious rights obscures the diversity of faith of LGBTI people."