Polling stations across the capital have just closed. NHK's projection is based on exit polls and information collected before the election.
Exit polls show Koike ahead of other candidates, including Ishimaru Shinji, former mayor of Akitakata City in western Japan's Hiroshima Prefecture, as well as former Upper House lawmaker Renho.
A former defense minister, 71-year-old Koike has served in both the Upper and Lower houses of Japan's Diet. She became Tokyo's first female governor in 2016.
During the campaign, Koike stressed the achievements of her two terms in the governor's seat. She also pledged more support to deal with the declining birthrate, saying the Metropolitan Government will expand its free childcare.
Koike faced a record 55 rivals in the gubernatorial race.
You may also be interested in: Campaigning kicks off in Tokyo governor race