Gustavo Salazar Delgado, the sport's number two official behind president Poul-Erik Hoyer, asked to be "excused from his duties", the BWF said.
"In his communication to BWF, Salazar indicated he would step aside for the time being so as not to cause any reputational or undue damage to the BWF while the investigation is in progress," the Kuala Lumpur-based body said.
The BWF said the accusations against Salazar related to "personal business matters" and are entirely unrelated to badminton and Salazar's role as BWF deputy president".
Bribery scandals linked to Odebrecht have swept up scores of Brazilian politicians and span several Latin American countries.
In April, a federal court in New York fined Odebrecht $2.6 billion, part of what US authorities describe as a one of the largest-ever corporate settlements for international bribery.
Salazar was re-elected unopposed as BWF deputy president last month. The BWF declined to provide more details when approached by AFP on Monday.
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