The Japanese government has proposed expanding and extending the country's state of emergency, with the Paralympics beginning on 24 August.
"We very much regret that this situation has impacted the Paralympic Games," organisers said in a statement.
As well as stadiums, fans were also requested not to attend road events.
Organisers confirmed spectators would not be allowed at events in Tokyo, Saitama, Chiba and Shizuoka because of infection rates in those regions.
