In the federal lawsuit, the NFLPA said the commissioner's ruling should be dismissed in favor of a ruling by an impartial arbitrator, The (New Orleans) Times-Picayune reported.
"The NFL has rendered the arbitral process a fraud, refusing to provide the NFLPA with access to relevant evidence or any witnesses while at the same time utilizing hearsay to smear and punish the players," the NFLPA attorneys said in the suit.
The lengthy suspensions given to current Saints Jonathan Vilma and Will Smith, as well as ex-teammates Anthony Hargrove and Scott Fujita, were justified in the pay-for-performance bounty program, the commissioner said Tuesday in rejecting the players' appeals.
Vilma received the harshest penalty -- suspension without pay for the entire 2012 season.
The suit said Goodell could not be an impartial arbitrator because before issuing the players' penalties, he "publicly proclaimed the players' guilt" and after that, but before the appeals hearing, had "repeatedly lauded the discipline he had imposed at the players' expense."
The NFL responded to the suit in an e-mail.
"There is no basis for asking a federal court to put its judgment in place of the procedures agreed upon with the NFLPA in collective bargaining. These procedures have been in place, and have served the game and players well, for many decades," the e-mail said.
In his decision, Goodell wrote of the four players, "Throughout this entire process, including your appeals, and despite repeated invitations and encouragement to do so, none of you has offered any evidence that would warrant reconsideration of your suspensions."
He asserted the four players "elected not to participate meaningfully in the appeal process" by refusing to make official statements or question their league accusers.
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