Krystsina Tsimanouskaya says she was forced to pack before being taken to the airport in Tokyo against her will.
The 24-year-old says she sought police protection at the terminal so she would not have to board the flight.
“I think I am safe. I am with the police,” she was heard saying, as she was pictured surrounded by officers.
The sprinter, who was due to compete in the women’s 200m event on Monday, had complained on social media about being entered into another race at short notice.
She says she was “put under pressure” by team officials to return home and asked the International Olympic Committee (IOC) for help.
“They are trying to get me out of the country without my permission,” she said in a video posted on the Telegram channel of the Belarusian Sport Solidarity Foundation (BSSF), a group that supports athletes jailed or sidelined for their political views.
The IOC said it was seeking clarification from Belarussian officials – who earlier said she was taken off the team because of her “emotional and psychological condition”.
In a later message, the IOC said it had spoken to Ms Tsimanouskaya. “She has told us she feels safe,” it said.
The flight took off without Ms Tsimanouskaya on board. She is now “safe” and in police protection, the BSSF’s Anatol Kotau told the BBC.
Earlier Ms Tsimanouskaya told radio station European Radio for Belarus (ERB) she was afraid to return to her country.