The Kenya Rugby Union (KRU) said it would investigate preliminary reports from the Ministry of Sports, detailing an alleged safeguarding incident involving the coach.
The board said Mwanja would take leave for two weeks "to enable investigations to be conducted fairly and transparently".
In a statement, the board said it had "zero tolerance for any form of inappropriate conduct, abuse of power," promising it would not shield individuals "whose actions violate the trust and well-being of our players."
There were no further details released.
Mwanja did not respond to AFP's request for comment.
He became the Kenya Lionesses sevens coach in 2022 and led the team to two subsequent finals of the Africa Women's sevens.
The team qualified for the 2016 Rio Olympics, as well as the 2020 Tokyo games, after South Africa declined the regional spot.
Arguably the second best on the continent, they finished second to South Africa in the 2025 women's rugby Africa Cup tournament in Madagascar in June.