In Saina's absence, fast rising shuttler P V Sindhu will represent India as lone singles player in the meet while P Kashyap will spearhead the men's team.
In all, an eight-member team has been selected for the event, starting September 17-22 in Tokyo.
"I will not be able to play in Japan. I am tired after playing in the IBL," Saina said.
Sania will next play in Denmark Open, where she is defending champion.
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Indian team for Japan Super Series:
Men: P Kashyap, Ajay Jayaram, Sai Praneeth, K Srikanth, Saurabh Verma, Manu Attri, Sumeet Reddy and P V Sindhu.
Coach: Madhumita Bisht.