Athletics head coach Yuri Moisevich and team official Artur Shumak were stripped of their accreditation and asked to leave the Olympic village in Tokyo, the IOC said in a statement on Friday.
Last week the pair were embroiled in a row with one of their own sprinters.
Krystsina Tsimanouskaya alleges the two men attempted to force her to return home following her criticism of sporting issues. She arrived in Warsaw, Poland, on Wednesday evening after she refused her coaches’ alleged instruction to return to her homeland.
She had refused to board a plane to Belarus and sought Japanese police protection. The sprinter was then offered a humanitarian visa by Polish authorities.
In an interview on Thursday, Ms Tsimanouskaya said the two officials had told her the order to send her home came from “high up” in Belarus.
The 24-year-old athlete’s case threatens to further isolate Belarusian President Alexander Lukashenko, who is under Western sanctions after a crackdown on opponents since last year, and whose son heads the national Olympic Committee.
“We are not the ones who made the decision, we are only executing it,” Ms Tsimanouskaya said the two officials told her. “You have 40 minutes. You have to pack your things and go to the airport.”
Mr Lukashenko’s spokesperson did not respond to a request for comment.
The two coaches would return to Minsk immediately, the Belarus Olympic Committee said in a statement on Friday, adding that they could appeal the decision and they hoped to continue a dialogue with the IOC.
IOC president Thomas Bach called Tsimanouskaya’s case “deplorable” on Friday and said the disciplinary commission would continue.
“We are happy Krystsina Tsimanouskaya is safe in Poland,” Mr Bach said.
Ms Tsimanouskaya said she decided to defect as she was being driven to a Tokyo airport because her grandmother told her that it was not safe to return home to Belarus.
She said she would testify in a disciplinary commission on Friday and urged the IOC to defend her and other athletes.
“I hope that the International Olympic Committee will make the right decision and will defend the athlete and defend me,” she said.
The IOC has come under scrutiny for failing to prevent the athlete from being removed from the games for expressing her views about coaching staff.
In the past, the Olympics organising body has acted swiftly to suspend athletes, officials or team members – even those with provisionally pending investigations – from the Olympics.
It took four days in the case of the Belarus coaches before they were ejected from the games.
Additional reporting by Reuters.
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