The NFLPA is seeking to collect $82,000 in workout bonuses from the former Patriot's contract. The tight end's deal was terminated by the team after he was arrested and charged with first-degree murder earlier this summer.
"On behalf of all players, it is our responsibility to protect the rights in the collective bargaining agreement," the union said in a statement. "We are not tone-deaf to what the allegations are in this case, but for the benefit of all players, there are important precedents here we must protect."
A team can recover bonus money and avoid a cap hit if a player violates one of the league's personal-conduct policies or defaults on contract language.
Patriots owner Robert Kraft responded to the grievance on Tuesday.
"Simple: you can look at our history. We honor all of our contracts, and we expect the people who sign them to honor their part of their contract," Kraft said, declining further comment.
Hernandez signed a five-year extension in August 2012 that was to keep him with the Pats through 2018. The extension had a total maximum value of $40 million with a $12.5 million signing bonus.
When looking solely at the signing bonus and base salaries, Hernandez earned $9.79 million of the extension.
The Bristol district attorney's office announced Tuesday that Hernandez is scheduled to be arraigned on Sept. 6 in Fall River (Mass.) Superior Court. He was indicted last Thursday.
Hernandez has previously pleaded not guilty in district court to murder in connection with the death of Odin Lloyd, who was found fatally shot June 17 near Hernandez's Massachusetts home. Prosecutors say Hernandez orchestrated Lloyd's killing because he was upset at him for talking to people Hernandez had problems with. Hernandez's lawyers say they are confident their client will be exonerated. Hernandez is being held without bail at a county jail.
Information from ESPN NFL Insider Adam Schefter, ESPNBoston.com's Mike Reiss and The Associated Press was used in this report.