Only 960,000 people were able to get their hands on at least one ticket for their favourite events out of the 5.12 million who had applied during the first domestic lottery in May.
Tokyo Olympics organisers launched a second ticket lottery on Thursday after unexpectedly high local demand forced them to reevaluate their Japanese sales strategy earlier this year.
Organisers said 5.12 million people had applied during the opening domestic lottery in May with only 960,000 able to get their hands on at least one ticket for their favourite events.
Over three million tickets were sold during that opening phase.
The more than four million applicants who were unsuccessful in that opening lottery will now have a second chance with some 680,000 tickets available in the supplementary lottery for sports including soccer, baseball and basketball.
Another wave of tickets will be made available for Japan residents in a lottery later this year before the final phase of sales in spring 2020.
Between 70 to 80 percent of all tickets have been reserved for domestic sale with the remainder allocated to international customers and sponsors.
Organisers said in their bid for the 2020 Games that 7.8 million tickets would be made available, though the exact figure has yet to be announced.