Yokozuna Kisenosato withdrew from the 15-day tournament at Tokyo's Ryogoku Kokugikan on Wednesday after posting a 6-4 record with a loss to Kotoshogiku on Tuesday.
"After seeing yesterday's results we decided he should withdraw as he is in no condition to produce decent sumo," his stablemaster Tagonoura said.
The 30-year-old Kisenosato electrified Japan's ancient sport by winning his first two tournaments since being promoted to the top-ranked yokozuna in January.
Previously, the last Japanese promoted to yokozuna was Wakanohana in 1998.
Kisenosato, who had missed just one day of competition since his sumo debut 15 years ago, sustained left shoulder injuries at the spring meet in March and has not recovered.
Mongolian yokozuna Hakuho and Harumafuji each have records of 10-0 to lead the summer tournament.