Koike, who was elected last month after two predecessors stepped down over scandals that clouded the city's Games preparations, was given the flag at the Rio Games closing ceremony on Sunday.
"Let's work together with everyone to hold a great Olympics and Paralymics as the Olympic flag, which just arrived, is a symbol of," she told reporters after waving the flag upon stepping off the flight at Haneda airport.
The Tokyo Games have been hit by series of issues including the scrapping of plans for the main stadium, which lead to delays in construction, and plagiarism allegations which forced organisers to ditch the original logo for the Games.
Koike was joined on the flight by Japanese athletes who took part in the Rio de Janeiro Games, where Japan won 12 gold medals - their best tally since 2004 - and a record 41 overall.
Keisuke Ushiro, who took part in the decathlon in Brazil, followed Koike off the plane waving a Japanese Olympic Committee flag.
(Reporting by Teppei Kasai. Editing by Patrick Johnston/Peter Rutherford)
