He complained about feeling pain after losing to Sam Querrey of the United States in the second round of the Shanghai Masters last Wednesday.
Nishikori said on Twitter that "I had an MRI on my right ankle and unfortunately will not be able to play Basel yet."
Nishikori lost in the final of last year's Swiss Indoors to Roger Federer. This year's tournament is scheduled to start Monday.
The 16th-ranked Nishikori beat Milos Raonic of Canada earlier this month to win the Japan Open for his second career ATP tour title and first in more than four years.
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