The agency said in a Thursday statement that Chevron paid the 35.1 million real ($17.3 million) fine last week for 24 of 25 irregularities detected. The statement did not provide details on the irregularities.
Some 155,000 gallons of crude are thought to have been released in the November 2011 spill.
The agency said it granted Chevron a 30 percent discount because it paid the fine on time and did not challenge it.
Chevron confirmed it paid the fine and said it will "implement a number of process improvements developed from lessons learned in the incident. Chevron Brasil respects and complies with the laws of the countries in which it operates."
The company said in a Friday statement that "continuous monitoring of the incident area shows no discernible environmental impact to marine life or human health."
Also on Friday, Brazil's state-run oil company, Petroleo Brasileiro SA, said it filed a suit in federal court asking for the suspension of an injunction ordering driller Transocean Ltd. to cease operations in Brasil until investigations into the spill are completed.
The company said in a statement that the suspension would hurt Petrobras' exploration activities since it is currently using seven Transocean rigs in Brazil.
Earlier this week, Transocean and Chevron were served injunctions ordering them to suspend operations in Brazil within 30 days.