Sharath Kamal went down without a fight 4-11, 5-11, 6-11, 11-13 against Jun in the pre-quarterfinals.
Earlier in the morning, Soumyajit Ghosh exited from the semifinals, going down in straight games to Hugo Calderano of Brazil in the U-21 singles.
The Brazilian, who won 11-9, 11-8, 11-4, 11-6 at Yokohama, has come a long way from his early shaky appearances to beat the Indian.
In fact, the Indian was kept on a tight leash right from the beginning by the classy Japanese and it took the toll on a normally fighting Sharath Kamal.
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Unfortunately, the Indian was rendered clueless on the day as Mizutani kept exploiting Sharath's weak backhands.
As for the u-21 semifinals, Hugo was all concentration on the day and it showed in his game. Matching stroke for stroke, he did not give much leeway to Ghosh who seemed good in the first two games.
Ghosh admitted to his folly of not continuing with his attacking game.
"I made far too many mistakes and could not reply as well as I should have to my rival. He seized the chances and scored many winners of my negative play," said Ghosh, who had beaten Hugo in the Brazil Open two years ago.
Peter Engel, the foreign coach, was happy with the way the Indians had prepared for the CWG Glasgow.
"The twin tour of Korea and Japan has given our paddlers a very good match practice and they have done reasonably well in the two top-class events. I am happy for their good showing," said the coach.