Morrison, who is making $414,000 this season, is seeking major league wages for the 10 days he was in New Orleans. If an agreement can't be worked out, a decision will be made by an arbitrator.
"It's not about money," Morrison said after hitting his 20th home run Thursday in Florida's 3-1 loss to the Phillies in the first game of a doubleheader. He struck out as a pinch hitter in the second game, which Philadelphia won 2-1 in 10 innings.
"I just want to put that behind me, but I also want to stand up for what's right. I consulted the players association and they felt we should file a grievance, not for just standing up for what's right, but protecting players' rights, my rights and people who come in after me."
Morrison was optioned after Florida's game on Aug. 13 to work on "being a major league player," baseball operations president Larry Beinfest said at the time.
Hours before the Aug. 13 game, Morrison skipped a team event with season-ticket holders on the advice of veteran infielder Wes Helms. Helms was released after the game.
Morrison returned to the starting lineup Thursday for the first time since Sept. 9, when he bruised his right knee. He did not start the second game of Thursday's doubleheader as a precaution.