Alan Joyce, the Qantas chief executive, has backed Rugby Australia’s actions in its dispute with former star player Israel Folau.

The dispute, which is now before the Fair Work Commission, was sparked by Rugby Australia ripping up Folau’s contract after he posted homophobic comments on social media despite being warned not to do so.

Joyce was speaking at the Qantas launch of two new routes – including the fourth-longest passenger flight in the world, from Brisbane to the US if regulators approve a new codeshare. Qantas is the Wallabies major sponsor.

Joyce told media that Folau’s comments were “clearly inappropriate” and added “we’re happy with how Rugby Australia is progressing this.”

“This is now the subject of Fair Work and legal action so we won’t comment any further.”

Folau was at the centre of controversy again on Monday after he used a sermon at his Sydney church to describe homosexuality as a sin and criticise young people being allowed to “change their gender”.

In a video posted to his church’s Facebook page, the former rugby union star claimed the devil was behind primary schoolchildren being allowed to decide if they wanted to change gender.

“They are allowing young kids in primary school, to be able to have the permission to change their gender if they want, by taking away the permission of their parents,” Folau said the Truth of Jesus Christ Church in Kenthurst.

“Now they’re trying to take control as a government to make those decisions for young kids, basically that are 16 years old or younger, they don’t even know what they’re doing ... this is what the devil’s trying to do to instil into this government, into this world, into society, and it’s slowly happening.

“The sad thing is why a lot of people out there that are non-Christians say bad things about the church, is because a lot of the churches allow those things to happen.

“They say that a man and a man should be able to be married and there is nothing wrong with it. This buys into the theme of pleasing man rather than pleasing God and standing up for the truth.”

The former Wallaby’s $5m Rugby Australia contract was torn up last month after he refused to take down an Instagram post which quoted bible scripture and said “hell awaits” homosexuals and other sinners.

In the new video, Folau also criticised modern “westernised” churches and said true believers in Christ “profess him wherever we go”.

“Are we too scared because we might be cast out by our workplace or cast out of somewhere because we’re not liked or loved by those around us and don’t believe the same thing we do?” he asked.

“You might be the only born-again Christian in that workplace, you might feel a bit awkward with your co-workers because they are in the world and you’re not. We should feel blessed … because God has called us.”

Folau has launched legal proceedings with the Fair Work Commission against Rugby Australia and is seeking up to $10m in damages.