According to news.com.auy, a Qantas spokesperson told foxsports.com.au that "as a sponsor of Rugby Australia, we're supportive of their approach towards tolerance and inclusion, which aligns with our own. We've made it clear to Rugby Australia that we find the comments very disappointing".
A devout Christian, Folau served as a face of the Bingham Cup, an amateur gay rugby tournament staged in Sydney in 2014.
But he first courted controversy last year when he publicly opposed same-sex marriage.
"I love and respect all people for who they are and their opinions. but personally, I will not support gay marriage," said the three-times John Eales Medallist as Australian rugby's test player of the year.
Folau's Super Rugby employers the NSW Waratahs consider the 29-year-old's religious beliefs his personal opinion.
But many social media users are less than pleased that "unlike Australia, Israel Folau isn't moving with the times."
Former Welsh star Gareth Thomas - professional rugby's first openly gay athlete - also took a swipe at Folau's comments.
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.