The two-time world champion's recent deal with Honda was set to include four tests in Japan with the aim of developing both Honda's factory 2014 MotoGP bike and the production racer it is selling to customer teams next year.
The rain this week forced the test team to stay at Motegi with Takumi Takahashi taking Stoner's place.
The Australian's next test is scheduled for October 2-3.
After Stoner's first test he confirmed that he did not plan to make a race return in MotoGP.
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