In a statement to The Associated Press, the city hall said Botafogo has been responsible for the utility bills since May 2015.
But the club told the AP that the city government owed it money to pay water and electricity bills.
The Brazilian newspaper Globoesporte said the unpaid bills totaled USD 250,000.
Brazil is in the middle of a deep recession, forcing cutbacks on Olympic organizers.
The Rio organizing committee said today it expected the stadium to be ready to host a test event in May, but referred questions to the club and city hall.