The players' union filed a grievance against the Mets and baseball's commissioner's office on Wednesday, Major League Baseball's official website (www.mlb.com) reported.
If the parties do not reach an agreement, an arbitrator will hear the case.
Rodriguez injured the thumb on his pitching hand during an altercation with the grandfather of his children at the Mets' stadium last week. He was arrested and charged with assault.
He underwent surgery on the right thumb on Tuesday, the same day the Mets placed him on the disqualified list and converted the remainder of his contract to a non-guaranteed one. He will not be paid until he returns unless the Mets' decision is overturned.
The club said it disagreed with the grievance filed by the players' union.
"We believe our action was justified and appropriate," the Mets said in a statement.
(Reporting by Gene Cherry; Editing by Sonia Oxley)