The organizers did not elaborate. Nadal was expected to address the situation on Friday.
Nadal was playing in the quarterfinals of the Swiss Indoors in Basel on Friday, his third tournament since Wimbledon, when a wrist injury curtailed his schedule.
The three will be replaced by Pablo Andujar of Spain, Jerzy Janowicz of Poland and Vasek Pospisil of Canada.
Nadal, third in world tennis rankings, has been struggling with appendicitis in recent weeks, although he has elected not to have surgery for the time being.
Nadal’s withdrawal also casts doubt over his participation at next month’s ATP World Finals in London.
Nadal faced Borna Coric in the Friday’s quarterfinals in Basel, Switzerland. He had planned to decide after that tournament whether to have surgery or conclude his campaign at the Tour Finals.
Contributing: Associated Press, Sportal.com.au