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The National Football League suspended New England Patriots quarterback Tom Brady for four regular-season games without pay "for conduct detrimental to the integrity of the NFL," the league announced Monday afternoon.

It also said that the team—which won the Super Bowl earlier this year—would be fined $1 million and forced to forfeit its first-round pick in the 2016 draft and its fourth-round selection in the 2017 draft.

The Patriots were accused following the AFC championship game in January of intentionally deflating footballs (which many players find easier to throw and catch). In explaining Monday's discipline announcement, the NFL said the team was penalized for "the violation of the playing rules and the failure to cooperate in the subsequent investigation."

Read MoreTom Brady: I did not alter the footballs

Brady's attorney, Don Yee, said his client will appeal the move.

"The discipline is ridiculous and has no legitimate basis," Yee said, in a statement. "The NFL has a well-documented history of making poor disciplinary decisions that often are overturned when truly independent and neutral judges or arbitrators preside, and a former federal judge has found the commissioner has abused his discretion in the past, so this outcome does not surprise me."

The Monday release said that Patriots owner Robert Kraft told NFL Commissioner Roger Goodell last week that two team employees had been indefinitely suspended without pay. The league said neither man could be reinstated without permission.

In a letter to the Patriots, NFL Executive Vice President of Football Operations Troy Vincent wrote that an investigation had found "the footballs used by the Patriots were inflated at a level that did not satisfy the standard set forth in the NFL's Official Playing Rules and that the condition of the footballs was the result of deliberate actions by employees of the Patriots."

Vincent said in his letter that the Patriots' employees' actions were documented in text messages and telephone communications.

Tom Brady #12 of the New England Patriots.
Getty Images

"In this case, the footballs were intentionally deflated in an effort to provide a competitive advantage to Tom Brady after having been certified by the game officials as being in compliance with the playing rules," Vincent wrote. "While we cannot be certain when the activity began, the evidence suggests that January 18th was not the first and only occasion when this occurred, particularly in light of the evidence referring to deflation of footballs going back to before the beginning of the 2014 season."

Vincent said that the investigation into the incident was impeded by Brady's "refusal to cooperate" when he was asked to produce evidence, and the fact that he was not "fully candid" during the process.

In a letter to the quarterback, Vincent wrote that the investigation "established that there is substantial and credible evidence to conclude you were at least generally aware of the actions of the Patriots' employees involved in the deflation of the footballs and that it was unlikely that their actions were done without your knowledge."

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In a January press conference on the allegations, Brady denied any wrongdoing. "I believe in fair play and I respect the league, and everything they're doing to try to create a very competitive playing field for all the NFL teams." Brady also said that "every team is trying to do the best they can to win every week."

"Your actions as set forth in the report clearly constitute conduct detrimental to the integrity of and public confidence in the game of professional football," Vincent added to Brady.

In 2007 the Patriots were sanctioned by the league for videotaping opposing coaches.

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—CNBC's Jessica Golden contributed.