The Japanese news agency Kyodo reported that two Uruguay players tackled staff members and damaged property at a bar in Kumamoto.
Kyodo said the business may file a criminal report.
The incident took place after Uruguay lost to Wales in the South American team's final Rugby World Cup pool match last Sunday.
"World Rugby is aware of an alleged incident involving members of the Uruguay team in a Kumamoto bar," the rugby body said in a statement on Thursday.
"The alleged matter is very disappointing and clearly does not align with the family spirit of the tournament."