Shoko Miyata, the 19-year-old captain of the Japan women's artistic gymnastics team, withdrew from the squad for the Paris Games after violating the team's code of conduct by smoking, the Japanese Gymnastics Association said.
JGA officials said Miyata arrived in Japan after leaving the team's training camp in Monaco for investigation, which confirmed the violation including drinking alcohol.
The women's squad will compete with four athletes instead of five, the JGA told a media conference.
"We apologize from the bottom of our hearts for this," JGA President Tadashi Fujita said, bowing deeply along with other officials including Miyata's personal coach, Mutsumi Harada.
Hopes had been high for the Japan women's gymnastics team, which was seeking to win a team medal at the Paris Games for the first time since the 1964 Tokyo Olympics.
Miyata had been expected to lead a team comprised entirely of first-time Olympians and teenagers after she secured her Paris berth in May with a third consecutive NHK trophy.
Coach Harada said that while Miyata's conduct had been reckless, she had been under extreme pressure to perform at the highest level.
"She was spending her days really burdened with so much pressure," he said, wiping away tears. "I would implore people to understand that."
Mental health facing young athletes took center stage at the last Olympic Games in Tokyo when gymnastics superstar Simone Biles pulled out of one competition after another.
Artistic gymnastics is one of the most popular sports at the Summer Games and will be held from July 27 to Aug. 5.