The government last month rejected Qatar's bid to run more flights to Australia, with Transport Minister Catherine King saying the request was not in the national interest.
Qatar Airways is owned by the Qatari government, which has been accused of human rights abuses.
But in a video message to staff, Virgin Australia chief executive Jayne Hrdlicka said the federal government's decision was disappointing and confusing.
"There's no understandable reason why they were denied those rights," she said.
"They're our partner, they served Australia well throughout COVID, and they're trying to continue to support Australians."
Opposition transport spokeswoman Bridget McKenzie accused the government of running a "protection racket" for Qantas by refusing to increase competition with the Qatar flights.
Qantas chief executive Alan Joyce has confirmed the company made a submission to the government seeking to block the Qatar flights but defended the move, saying other carriers had added a "massive amount" of capacity to the market.
Ms Hrdlicka said a lack of competition and flight capacity was keeping international airfares high.
"Prices have been as high as two times 2019 levels," she said.
"Qatar is one of the only airlines in the world that could overnight put four additional services per day into Australia and for some reason they were denied."
The chief executive said more Qatar flights would have brought an additional $500 million to Australia's tourism sector, especially in Queensland.
"This decision means less jobs, less opportunity, and denied growth for a part of the economy that suffered most during COVID," Ms Hrdlicka said.
A Virgin Australia spokeswoman confirmed the video was sent to staff on Thursday, adding it was important to increase aviation capacity between Australia and the rest of the world.
"We look forward to working with the federal government and other key stakeholders to find a way to understand and resolve the underlying issues," the spokeswoman said in a statement to AAP.
Mr Joyce will on Monday appear before a Senate committee on the rising cost of living.
Competition in the airline industry is expected to feature during questioning.
