Both the men's and women's races have been moved more than 800 kilometres north to Sapporo due to fears about high temperatures.
The races would have been free to watch on the streets of Tokyo but a ticket guaranteed a seat in the New National Stadium for the finishes.
Fans have now been e-mailed about applying for a refund.
For the men's event this should be a simple process as tickets only covered the finish of the race.
It is more complicated for the women's race as the finish was due to be part of a full session of track and field, which the tickets still cover.
Fans affected by this can opt to receive a full or partial refund on what they paid.
Race walking events were also moved to Sapporo due to the concerns about heat, but the decision to move events prompted a backlash from athletes and officials.
Critics included Tokyo Governor Yuriko Koike, who called the decision "unprecedented".
She said heat-prevention measures were in place in the capital, with the city now set to lose money and miss out on exposure.
The Japan Association of Athletics Federations called the move "regrettable" and many athletes claimed the change of plans would impact their training.
International Olympic Committee officials have insisted, however, that the move was down to athlete safety fears.
More than 50 deaths were recorded in Japan because of the heat in July of last year, with the Tokyo 2020 Olympics scheduled for between July 24 and August 9.
The late switch to Sapporo has necessitated a schedule change for the women's marathon, which was initially planned for August 2 but has been pushed back six days to August 8.
The men's marathon will remain on August 9, the day of the Closing Ceremony where the medal ceremony traditionally takes place.
Tokyo 2020 has warned that this will cause logistical issues.
Both marathons will now end at Sapporo's Odori Park, and will be free to watch.
The Hokkaido city hosted the 1972 Winter Olympics and has been tipped to host the Games again in 2030.
(Article from Inside the Games)