A joint statement issued by RA and the NSW Rugby Union said it supported the "all forms of inclusion".
RA Chief Executive Raelene Castle and Waratahs boss Andrew Hore will meet the 29-year-old to discuss his use of social media.
"Israel's comment reflects his personal religious beliefs, however it does not represent the view of Rugby Australia or NSW Rugby," Castle said in a statement on Thursday.
"We are aligned in our view that Rugby is a game for all, regardless of sexuality, race, religion or gender, which is clearly articulated in Rugby's inclusion policy.
"We understand that Israel's comment has upset a number of people and we will discuss the matter with him as soon as possible."
Folau said last year that he would not support legislation of gay marriage during nation-wise plebiscite.
Australia's parliament voted to legalise same-sex marriage in December after the vote returned an overwhelming majority in favour of same sex unions.
(Reporting by Hardik Vyas in Bengaluru; editing by Sudipto Ganguly)
