Speaking at a news conference to promote his charity golf tournament, the 2010 Super Bowl MVP said there's a difference between pay-for-performance and pay-for-injury.
Brees also declined to say whether he'd show up for offseason workouts that begin Monday. He'd much rather have a long-term extension than the franchise tag he's been slapped with.
Brees was asked if he felt he had been a target of a bounty program during his career.
"I know this, that 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 that he's trying to end your career, that he's trying give you a concussion or what have you, but between the knees and the neck, they're trying to take you out every time. I know that for a fact, every defensive player that's trying to hit you. That's just football. We play a violent game."
Then, he added: "I am not condoning by any means any kind of a bounty structure, and I will clarify that there is a difference between pay-for-performance and pay-for-injury, and I'd say what we've been accused of in regards to pay-for-injury is not the case."
"I think that was hard for everybody to hear," said Brees, who tried to shift the talk back to his golf tournament.
Brees said the Saints are disappointed that NFL Commissioner Roger Goodell rejected on Monday an appeal of Payton's season-long suspension for his role in the bounty program.
"You talk about not having your head coach for an entire season, that's a big hit," said Brees, who declined to say who'd he like to see hired as interim coach.
But Brees said he believes the Saints will remain strong. He pointed to last year, when Payton was injured in a sideline collision and had to coach several games from the press box. While he was used to having Payton call in the plays, all of a sudden he had to get used to offensive coordinator Pete Carmichael Jr. calling them in.
"It was almost as if our head coach had been taken away for a four-to-six week period," Brees said.
"It seems like our organization, whenever we're hit with something, any kind of adversity, we have guys that step up and fill the void and take on more responsibility and really thrive in it," he said. "We did it last year and whatever is thrown at us this year we'll continue to thrive."
As for his contract and whether he'd show up Monday, Brees said: "We're continuing to work on a long-term deal and we're very hopeful that we can accomplish that sooner than later."
Brees spoke at La Costa Resort & Spa while promoting his Drew Brees Celebrity Championship, which will be played in May.
Brees said he'd like to beat Romo but, "I think he's been playing more golf than me." In past years, Romo has attempted to qualify for the U.S. Open.