In some regional seats including Indi where there is a strong independent candidate, the commission expects the figure to be up to 55 per cent.
In 2007, just 14 per cent voted early.
Mr Rogers said the growing popularity of early voting was changing the nature of elections, diluting the traditional campaign focus on election day.
“If you’re getting up to 50 per cent [voting early] rather than voting on the day it really is leaching into a voting period,” he said.
Nationally, 31.25 per cent of voters voted early in the last federal election in 2016; in Victoria it was 39 per cent.
AEC state manager Steve Kennedy said the commission fully expected the proportion to keep rising.
“We anticipate that’ll go up to about 43 per cent, but in seats like Ballarat, Nicholls [formerly Murray] and Indi, we anticipate up to 55 per cent of electoral voting before polling day,” Mr Kennedy said.
The parties will also have to reckon with a surge of 132,000 first time voters who signed up during the same sex marriage postal survey.
Mr Rogers said most of the «extraordinary» influx of new enrolments from the plebiscite period were in the 18-24 age bracket, putting the youth enrolment rate at what is most likely an all-time high.
In Victoria, those enrolments were most heavily concentrated in a ring of inner-city electorates including Melbourne, Macnamara (formerly Melbourne Ports), Kooyong and Wills.
The trend towards early voting does not appear to signify growing disengagement with politics.
Australia-wide, a record high 96.3 per cent of eligible voters are on the electoral roll, up from 90 per cent in 2010.
The commission is due to launch a promotional campaign this week targeting almost 500,000 people who are not on the electoral role.
The Morrison government is expected to call the federal election for May.
State Political Correspondent for The Age