The International Olympic Committee (IOC) confirmed that Artur Shimak and Yury Maisevich had left the Olympic Village. An investigation is under way.
The case of Krystina Timanovskaya caught global attention after she refused her team’s orders to fly home.
Belarus says she was removed from the national team because of her emotional state. But the 24-year-old says this is not true, saying she was removed because she spoke on Instagram about the “negligence of [her] coaches”.
In a statement, the IOC said it had removed the accreditations of the two coaches “as a provisional measure… in the interest of the wellbeing of the athletes of the National Olympic Committee of Belarus who are still in Tokyo”
The body said a disciplinary commission had been established to investigate the incident and that both coaches would be “offered an opportunity to be heard”.
The case has again put the spotlight on Belarus, which has been ruled by authoritarian President Alexander Lukashenko since 1994. Last year, nationwide protests over his disputed re-election were violently repressed by the security forces.
Ms Timanovskaya’s removal came after the sprinter complained on social media about being entered into the 4x400m relay race at short notice, after some team-mates were found to be ineligible to compete.
The video led to criticism in state media, with one television channel saying she lacked team spirit.
In an interview with the BBC, she said she was on her way to the airport last week when her grandmother warned her it was not safe to return, after watching local news reports on the situation.
She was then given police protection before being moved to the Polish embassy in Tokyo. She travelled to Poland on Wednesday.
Some of the protesters were national-level athletes, who were then stripped of funding, cut from national teams and detained.
But Ms Timanovskaya insists that she is “not a political girl” and just wants to focus on her sporting career.