The Patriots parted company with Hernandez following his arrest for the alleged murder of Odin Lloyd in June.
However, the NFLPA believe that Bill Belichick's side owe Hernandez $82,000 (£53,000) after he participated in his side's off-season activities prior to his incarceration.
A statement said: "On behalf of all players, it is our responsibility to protect the rights in the collective bargaining agreement.
"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 which we must protect."
Hernandez was indicted by the Grand Jury on a first-degree murder charge last week in North Attleboro, Massachusetts.