Outgoing Qantas boss Alan Joyce has rejected allegations the federal government is in his pocket, after an application from Qatar Airways to add flights to Australia was rejected without explanation.

Qantas rival Virgin Australia has a close partnership with Qatar Airways and would have benefited from additional flights through its code-share relationship with the airline.

Joyce said he had often opposed the Albanese government, including whether to introduce multi-employer bargaining, and the outcome had not gone in the airline’s favour.

“The chief executive of Qantas or Virgin will always have a relationship with the government,” Joyce said on Thursday. “There are a lot of things I disagree with the government on, as well as lots we do agree on. That’s the way it works. It is just nonsense that we have unbelievable influence and I don’t know how that mindset has developed.

“If the government was doing the bidding of Qantas it wouldn’t have gone with multi-employer bargaining which is a much bigger issue,” Joyce said. “The prime minister had a go at me when we grounded the airline in 2011. To think that Qantas has this out-weighted influence on them is nonsense.”

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Joyce was speaking after appearing on a panel with Virgin Australia chief executive Jayne Hrdlicka and hosted by Virgin founder Brett Godfrey, who now chairs Tourism and Events Queensland.

Joyce declined to comment on whether Albanese’s son – Nathan Albanese – had been extended an invitation to the Qantas chairman’s lounge, as reported in The Australian Financial Review. The airline does not divulge who is invited into the exclusive lounge, which is usually reserved for executives of large companies and politicians.

“I’ve been good mates with Albo for some time, but the assumption that whatever I do would get political favours is not happening,” he said.