The union is fighting the league to collection Hernandez's cash after he signed a five-year $40 million contract extension last year.
In addition, the NFLPA previously filed a grievance to help Hernandez for $82,000 workout bonus, according to The Associated Press. Hernandez's contract says he would receive that amount if he participated in 90 per cent of the team's voluntary offseason workouts.
The NFL's collective bargaining agreement allows teams to recuperate bonus money when a player is jailed though, and Hernandez is currently being held without bond on first-degree murder and weapons charges in the death of Odin Lloyd.
The Patriots cut Hernandez before that bonus, if earned, was due.
"On behalf of all players, it is our responsibility to protect the rights in the collective bargaining agreement," the union said. "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."
Patriots owner Robert Kraft disagreed.
"It's simple," Kraft told The Associated Press. "You can look at our history. We honour all our contracts and we expect the people who sign them to honour their part of the contract."