The equality commission has called statements "against the recognition of same-sex families" may lead to unequal treatment of persons based on their perceived sexual orientation, or gender identity.

The National Commission for the Promotion of Equality (NCPE) issued its statement following reports of claims by Auxiliary Bishop Charles Scicluna, who has been a vocal critic of the government's plans to introduce civil unions and gay adoption.

"The NCPE promotes the right to freedom of thought, conscience and religion, and calls on the relevant authorities to ensure the right of persons, regardless of sexual orientation or gender identity to hold and practice religious and non-religious beliefs," the NCPE said in a statement.

"Government and relevant authorities should also ensure that the expression, practice and promotion of different opinions, convictions and beliefs with regard to issues of sexual orientation or gender identity are undertaken in a manner compatible with human rights."

The NCPE said that whilst everyone had the right to freedom of opinion and expression, the rights and freedoms of others should be respected.

"The NCPE believes that everyone has the right to found a family, including access to apply for adoption or assisted procreation, regardless of sexual orientation and/or gender identity. The NCPE encourages the government to take all necessary legislative, administrative and other measures to ensure that no family may be subjected to discrimination on the basis of sexual orientation and/or gender identity."