Tsimanouskaya, masked and wearing blue jeans, a blue blouse and sunglasses, arrived in a police-escorted van at Narita airport east of the Japanese capital at 8:27 a.m. (2327 GMT on Tuesday) and did not talk to waiting reporters.
Her refusal to board a flight home late on Sunday, after she said she was taken by her team to the airport against her wishes, caused high drama at the Games. She sought protection at at the embassy on Monday.
She was expected to go to Poland, her supporters have said. Warsaw has offered her a humanitarian visa.