The two-time world champion tested positive during a mandatory PCR test at Narita Airport in Tokyo, as the team were assembling to fly to Thailand on Sunday (3rd January), according to the BWF.
The top Japanese men and women had gathered at the National Training Centre in Kita a day earlier and been due to compete in the Yonex Thailand Open (12-17 January) and Toyota Thailand Open (19-24 January).
Other Japanese men due to compete in Bangkok were Tsuneyama Kanta, Nishimoto Kenta, and Watanabe Koki.
Momota is currently world number one, and had been top seed for the Yonex Thailand Open.
The 26-year-old is one of the home favourites for gold at the Tokyo Games in 2021.
Organisers of the 'Asian Leg Bubble' tournaments in Bangkok confirmed the events would still take place, with replacement players being invited from the list of reserves.
China had already withdrawn its teams from both tournaments due to coronavirus concerns.
The BWF World Tour Finals 2020 are due to take place 27-31 January 2021, also in Bangkok.
Momota had claimed his third consecutive All Japan title in Tokyo on Sunday 27 December, his first event back after suffering a car crash at the start of 2020.