Scott Green, executive director of the NFL Referees Association, acknowledged Ellison's reinstatement in a statement to ESPN on Friday, saying the union may file a grievance over it.
"Roy is back on the field where he should be and the union will consider filing a grievance objecting to this fine," Green said.
A source told ESPN that Ellison's fine was for one game check -- $9,300. NFL Network first reported the amount of the fine.
The NFL previously fined Hughes $53,482 for unsportsmanlike conduct for confronting Ellison in the tunnel of Hard Rock Stadium after a loss to the Dolphins. The amount of Hughes' fine was dictated by the NFL's collective bargaining agreement with the NFL Players Association for a second offense of verbal or other non-physical offense against an official.
In video of the confrontation, Hughes accused Ellison of calling him a "b----." The ninth-year defensive end was later restrained by a team staff member and a teammate as he continued to shout at the official, "I'll catch you!"
Ellison, in his 16th year as an NFL official, was previously suspended one game without pay in 2013 for allegedly making a profane and derogatory statement to Washington Redskins offensive lineman Trent Williams.
Following that 2013 game against the Philadelphia Eagles, Williams said Ellison cussed him out during a Redskins drive late in the first half, an accusation teammates backed. Williams said Ellison walked by him after a play and called him a "garbage-ass, disrespectful m-----f-----."
Hughes denied the confrontation to reporters in the locker room shortly after. He also said he did "not recall" whether an official called him a "b----" during the game.