The move came a day after the club converted Rodriguez's contract to non-guaranteed, placed him on the disqualified list and announced it would not pay him while he was unable to perform.
The case could get to arbitrator Shyam Das within two to three months if it goes unsettled beforehand.
The Mets maintain Rodriguez tore a ligament in his right thumb during an altercation with his girlfriend's father at Citi Field last week. Chief operating officer Jeff Wilpon said Tuesday that Rodriguez confessed to a team trainer that the injury occurred as a result of the incident.
Rodriguez's agent, Paul Kinzer, and the union have been noncommittal about when the injury occurred. And a team source told ESPNNewYork.com on Wednesday that Rodriguez will claim he slipped, but not as a direct result of the incident.
Rodriguez is accused of grabbing 53-year-old Carlos Pena, hauling him into a tunnel near the family lounge beneath Citi Field and hitting him in the face. Pena was taken to a hospital with a scrape and swelling above his eyebrow. Rodriguez faces third-degree assault and second-degree harassment charges.
A union source said the players' association is convinced the Mets' attempt to place Rodriguez on the disqualified list and the conversion of the contract to non-guaranteed will be overturned by the arbitrator. The source added that the union is confident Rodriguez's lost salary for the remainder of the season -- with the exception of the $125,683 lost for the original two-day suspension that was negotiated with the players' association -- will be recovered.
The Mets issued a statement regarding the grievance.
"We disagree with the position of the Players Association," it read. "We believe our action was justified and appropriate."
By going on the disqualified list, Rodriguez will lose $3,016,393 of his $11.5 million salary this year.
Rodriguez underwent surgery Tuesday to repair the torn thumb ligament. The Mets expect him to be ready to contribute during spring training.
If making Rodriguez's contract non-guaranteed stands after the arbitrator's ruling, that would allow the Mets to cut him loose during either of the next two spring trainings and be responsible for as little as 30 days' pay. That could be a vehicle for the Mets to get out of an onerous $17.5 million vesting option for 2012 that would kick in if Rodriguez finishes 55 games next season and is healthy at the end of the year.
Rodriguez is due to make $11.5 million next season. There's also a $3.5 million buyout if the vesting option terms are not achieved.
Adam Rubin covers the Mets for ESPNNewYork.com.