Brees said at a news conference in Carlsbad, Calif., for his May charity golf tournament that a distinction needed to be made between "pay for performance" and a reward system for injuring players.
"I would say what we've been accused of in regards to pay for injury is not the case," Brees said.
Brees also explained that when he tweeted last month he was "looking for an explanation" after NFL Commissioner Roger Goodell announced the penalties against the team, he was only questioning the season-long suspension of coach Sean Payton.
"I was talking about my head coach. I wasn't referring to anybody else," said Brees, who also told reporters he had yet to receive an explanation for Payton's punishment.
Brees added that the audio of former Saints defensive coordinator Gregg Williams encouraging his players to injure specific San Francisco 49ers players before a playoff game "was hard for everybody to hear."
Asked if "bounty" systems are prevalent in the NFL, Brees said he believes defensive players are aggressive by nature.
"I know this: When a guy has an opportunity to take a shot at the quarterback, he's going to take it," Brees said. "I'm not saying he's trying to end a career or give you a concussion. But between the knees and the neck, he's trying to take you out every time. That's just football -- we play a violent game."
Since Goodell announced Monday that he had decided to uphold the penalties against the Saints, Brees hadn't heard of any possible replacements for Payton for the 2012 season. With Bill Parcells electing to remain retired, the Saints will promote from within the organization for an interim coach, a league source told NFL Network insider Jason La Canfora on Tuesday.
In addition to Payton's suspension, assistant head coach Joe Vitt has been suspended six games and general manager Mickey Loomis has been suspended for eight games. Williams, who's now with the St. Louis Rams, hasn't appealed his indefinite suspension.