The team will attend a training camp in the city of Ota before moving to the Athletes' Village in Tokyo on 17 July.
All members of the delegation have been vaccinated against Covid-19 and will be tested for the virus every day.
The Games are scheduled to begin on 23 July despite Japan battling a surge in coronavirus cases.
While in Ota the Australia squad, who all tested negative for the virus upon arrival in the country, will be confined to one floor of their hotel and will only be able to leave the building to train.
Large parts of Japan including Tokyo are under a state of emergency until 20 June, although International Olympic Committee vice-president John Coates said last month that the Games would still go ahead even if restrictions remained in place.
A friendly football match between Japan and Jamaica on Thursday has been cancelled after 10 Jamaica players were unable to board a flight from Europe because of coronavirus testing issues.
Olympic Minister Tamayo Marukawa also says 105 Japanese municipalities have cancelled plans to host overseas teams before the Games, mainly because the delegations will now go directly to the Athletes' Village in Tokyo instead.
More than 60% of respondents to a recent poll were in favour of postponing the Games again or cancelling it altogether.
The Japanese government is speeding up its vaccination drive in the run up to the event, with vaccinations of Japan's Olympic athletes beginning on Tuesday.
Vaccinations at workplaces and universities will start on 21 June, with only around 3% of Japan's population currently fully vaccinated against Covid-19.