RA announced that chief executive Raelene Castle and Waratahs boss Andrew Hore would meet with Folau following a statement he made on Instagram.
Australia's highest-profile player, who is a devout Christian, sparked social media outrage on Wednesday when he said gay people were headed to "HELL ... Unless they repent of their sins and turn to God" in response to a question on Instagram.
The governing body said "Folau's personal beliefs do not reflect the views of Rugby Australia" as a flurry of Twitter users questioned whether Qantas -- a vocal supporter of same-sex marriage -- should align itself with the Wallabies and, by association, Folau.
Castle said both organisations were treating the matter seriously.
"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.
"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."
The latest comment, which comes six months after Folau tweeted that he opposed gay marriage, puts RA in a difficult predicament.
The 62-Test star is off contract at the end of this year, with Wallabies coach Michael Cheika desperate to secure his attacking trump for next year's World Cup in Japan.
Folau deleted the post but a screen shot allowed other social media users -- including the fullback's 337,000 Instagram followers -- to see the provocative exchange.
Many social media users were less than pleased that "unlike Australia, Israel Folau isn't moving with the times".
"Does Qantas or the qantaswallabies have any comments on IzzyFolau stating that all gay people are going to hell. Is that a core belief of Qantas and the Wallabies?" another user asked.
Another posted: "Qantas As a major Sponsor for the wallabies are you ok with IzzyFolau homophobic outburst. Considering a significant amount of your staff are Gay?? I think you should drop the sponsorship."
Folau, three-times John Eales Medallist as Australian rugby's Test player of the year, served as a face of the Bingham Cup, an amateur gay rugby tournament staged in Sydney in 2014.
Now he has seemingly contravened RA's inclusion policy.
"Rugby has and must continue to be a sport where players, officials, volunteers, supporters and administrators have the right and freedom to participate regardless of gender, sexual orientation, race or religion and without fear of exclusion," the policy states.
"There is no place for homophobia or any form of discrimination in our game and our actions and words both on and off the field must reflect this."