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After a lengthy investigation conducted by the NFL's security department, the league announced Friday that 22 to 27 defensive players on the New Orleans Saints maintained a "pay for performance" program that included "bounty" payments administered by then-defensive coordinator Gregg Williams during the 2009, 2010 and 2011 seasons.

The program runs in violation of league rules, and the investigation showed that Saints players received $1,500 for a “knockout” hit and $1,000 for a “cart-off” hit with payouts doubling or tripling during the team's three playoff appearances. The program also entailed payments for interceptions and fumble recoveries, which also violates league rules against non-contract bonuses. NFL Commissioner Roger Goodell will determine the appropriate discipline based on the investigation, the league said in a statement.

"The payments here are particularly troubling because they involved not just payments for ‘performance,’ but also for injuring opposing players,” Goodell said in a statement released by the league. “The bounty rule promotes two key elements of NFL football: player safety and competitive integrity.

“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.”

Goodell said the investigation began in 2010 after allegations were made that the Saints defenders had targeted Arizona Cardinals quarterback Kurt Warner and Minnesota Vikings quarterback Brett Favre during their 2009 run to the Super Bowl.

"Our security department interviewed numerous players and other individuals," Goodell said. "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.”

The investigation found the program was funded primarily by players and at one time might have reached $50,000. The league also said that other defensive coaches in addition to Williams, now the St. Louis Rams defensive coordinator, were aware of the program.

The report found that Saints head coach Sean Payton was aware of the allegations but didn't act on them.

Payton "was not a direct participant in the funding or administration of the program," according to the investigation. However, Payton "was aware of the allegations, did not make any detailed inquiry or otherwise seek to learn the facts, and failed to stop the bounty program. He never instructed his assistant coaches or players that a bounty program was improper and could not continue," the investigation found.

The league also said that general manager Mickey Loomis at one time was directed to end the program when team owner Tom Benson was made aware of the league's findings, and he did not carry out Benson's directions.

"I have been made aware of the NFL’s findings relative to the 'Bounty Rule' and how it relates to our club," Benson said in a statement. "I have offered and the NFL has received our full cooperation in their investigation. While the findings may be troubling, we look forward to putting this behind us and winning more championships in the future for our fans."

The investigation included the review of approximately 18,000 documents totaling more than 50,000 pages, interviews of a wide range of individuals and the use of outside forensic experts to verify the authenticity of key documents.

The Saints have gained a reputation in league circles as a dirty team in recent years, and Vikings running back Adrian Peterson said this past season that the Saints targeted his high left ankle sprain.

"I felt like it kind of got overboard," Peterson said at the time. "I got up and kind of got in his face. Thank God I was able to keep my composure."

The Saints denied Peterson's claims.

Warner was asked about the issue during an appearance on KTAR radio in Phoenix today and said, "It's disappointing but I won't say I'm completely surprised."

Warner was knocked out of the game on a big hit from Saints defensive end Bobby McCray, but Warner emphasized the hit was legal.

The following weekend, the Saints repeatedly battered Favre in the NFC title game.

As Profootballtalk.com’s Mike Florio suggested, the league’s announcement that the Saints violated the “bounty” rules sends a clear message to the Saints and every other team regarding the fact that such activities won’t be accepted. But what message does this entire situation end regarding the Super Bowl victory the Saints earned at the end of a playoff run fueled by extra payments for injuring opposing players?

Perhaps the disciplinary actions that will be taken by the league will answer that question.

According to ESPN insider Adam Schefter, discipline for the Saints could include fines, suspensions and forfeiture of draft choices. Those fines and suspensions will start at the player level and will move through the team's coaching staff and front office -- all the way to ownership.

And remember: Goodell has made it clear that coaches and management will be held to a higher standard than players when it comes to issues like this.

Bottom line? As Schefter summed up: "The Saints will be disciplined far worse than the Patriots were for Spygate."

UPDATES: Subsequent reporting has suggested that Williams ran a similar program during his stint as Redskins' defensive coordinator .

Williams also released a statement apologizing for what he called a "terrible mistake."

Additional reporting suggests that Loomis could be in serious trouble. Payton, too. ...

Despite their difficulties, Loomis and Payton apparently still have Benson's full support.

The NFL will investigate the allegations involving the Redskins.

They might also have to investigate allegations involving the Bills, where Williams served as head coach

Meanwhile, FOXSports insider Jay Glazer reports the league's decision on disciplinary measures should be announced by March 25.