In a lengthy news release, the league said the Saints maintained a bounty program during each of the last three seasons.
NFL Commissioner Roger Goodell said the payments were administered by New Orleans Defensive Coordinator Gregg Williams, with the knowledge of other defensive coaches. The commissioner said when Saints owner Tom Benson learned of the payments he put a stop to them.
The league said head Coach Sean Payton did not participate in the payments, but was aware of them.
Goodell will eventually be responsible for determining what penalties the franchise and individuals will face.
"The payments here are particularly troubling because they involved not just payments for 'performance,' but also for injuring opposing players," Goodell said. "It is our responsibility to protect player safety and the integrity of our game, and this type of conduct will not be tolerated. We have made significant progress in changing the culture with respect to player safety and we are not going to relent. We have more work to do and we will do it."
The NFL said players contributed cash into a pool and payments from the pool were made based on performances in each game.
The investigation showed payments were made for interceptions and fumble recoveries, but payments were also made when an opposing player was carried off the field or knocked out of the game.
Such payments doubled and tripled during the playoffs.
The NFL said its investigation involved interviews that produced more than 50,000 pages of transcripts.
League rules forbid players from accepting bonus money that is not included in their contracts.
"Our investigation began in early 2010 when allegations were first made that Saints players had targeted opposing players, including Kurt Warner of the Cardinals and Brett Favre of the Vikings," Goodell said. "Our security department interviewed numerous players and other individuals. At the time, those interviewed denied that any such program existed and the player that made the allegation retracted his earlier assertions.
"As a result, the allegations could not be proven. We recently received significant and credible new information and the investigation was re-opened during the latter part of the 2011 season."