A left thigh injury forced the 17-year-old to withdraw from the national championships, which act as the qualifying meet for Rio, the Kyodo news agency reported.
"I am really disappointed, I have just got to try and do my best to aim for the Tokyo 2020 Olympics," Sani Brown said.
Sani Brown clocked 10.28 seconds in the 100 metres and 20.34 in the 200, the second bettering the mark set by Usain Bolt in 2003, to claim the sprint double at the youth championships in Colombia and also won the IAAF Rising Star Award in 2015.
He became the youngest athlete to represent Japan at senior level at the world championships in Beijing, where he reached the semi-finals of the 200m.
His coach Takahiko Yamamura said: "He had a burning desire (to compete in Rio) and I feel bad that I can't have him at the starting line."
(Writing by Sudipto Ganguly in Mumbai; Editing by John O'Brien)
