Alana Joyce added that he believes the requirement will become common around the world.
The Sydney-to-Melbourne is the world's second-busiest air route and Australian lawmakers are keen to revive domestic travel and tourism in a bid to revive the ailing economy.
However, international travel remains tricky - with many countries imposing mandatory quarantines on tourists.
He added that he expects a vaccination requirement for international air travel to become common around the world.
“I think that’s going to be a common thing talking to my colleagues in other airlines around the globe", he said.
Australia also hopes to restart international travel with flights to New Zealand in the works.
While New Zealand citizens can now travel to Victoria without quarantining, a reciprocal agreement is still some way off. New Zealand says Australians will remain barred until the entire country has gone at least 28 days without a single Covid-19 case.
Australia's economy shrank 7 per cent in the three months that ended in June, the most since records began in 1959, while the unemployment rate hit a 22-year high of 7.5 per cent in July.