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The B-Max Racing/Motopark team made the decision to withdraw its sole entry for the 2020 curtain-raiser after Natori fell ill following Saturday's opening Super Formula Lights race.
Natori had struck a last-minute deal to make his Super Formula debut at Motegi, as both of the B-Max/Motopark squad's regular drivers Sergio Sette Camara and Charles Milesi could not make it to Japan due to travel restrictions.
However, this resulted in a punishing schedule for the 19-year-old, who is also racing this weekend in Super Formula Lights for Toda Racing - made even tougher by the sweltering heat at Motegi, which basked in temperatures of 34 degrees on Saturday.
After being taken to the medical centre following his third-place finish in the support category's first race, Natori was given clearance by doctors to drive in Sunday morning's final practice session and qualifying in Super Formula.
However, after he qualified 18th of the 19 runners, B-Max/Motopark opted to withdraw Natori's entry, reducing the size of field to 18 cars.
Natori finished seventh in Sunday morning's second Super Formula Lights race of the weekend and he is expected to take part in the final race, which takes place immediately after the 35-lap Super Formula event, as planned.
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